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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Bcbio_nextgen installation doesn't create symlinks to executables from all the environments into bcbio_nextgen/tools/bin #2711

Closed amizeranschi closed 5 years ago

amizeranschi commented 5 years ago

Hi,

Not sure if this is intended, but I noticed that executables from some of the conda environments aren't getting symlinked into bcbio_nextgen/tools/bin. The ones from the bcbio-vm environment stood out to me, but others could be missing as well.

In case it helps shed more light on this, below is a list of all the files that are in bcbio_nextgen/tools/bin:

$ ls -l /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/tools/bin/
total 0
lrwxrwxrwx 1 amizeranschi amizeranschi 21 Mar  3 15:55 7z -> ../../anaconda/bin/7z
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 7za -> ../../anaconda/bin/7za
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 7zr -> ../../anaconda/bin/7zr
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 abba-baba -> ../../anaconda/bin/abba-baba
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 ace2sam -> ../../anaconda/bin/ace2sam
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 addadapters.sh -> ../../anaconda/bin/addadapters.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 age_align -> ../../anaconda/bin/age_align
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 alignmentSieve -> ../../anaconda/bin/alignmentSieve
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 alleleCounter -> ../../anaconda/bin/alleleCounter
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 16:06 alleles -> ../../anaconda/envs/python2/bin/alleles
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 AMBER -> ../../anaconda/bin/AMBER
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 AnalyseDists -> ../../anaconda/bin/AnalyseDists
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 AnalyseSeqs -> ../../anaconda/bin/AnalyseSeqs
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 15:55 analyzeaccession.sh -> ../../anaconda/bin/analyzeaccession.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 annotateBed -> ../../anaconda/bin/annotateBed
lrwxrwxrwx 1 amizeranschi amizeranschi 51 Mar  3 16:06 annotate_vcf_bam.py -> ../../anaconda/envs/python2/bin/annotate_vcf_bam.py
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 a_sample_mt.sh -> ../../anaconda/bin/a_sample_mt.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 16:08 atropos -> ../../anaconda/envs/python3/bin/atropos
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 aws -> ../../anaconda/bin/aws
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 aws_bash_completer -> ../../anaconda/bin/aws_bash_completer
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 aws.cmd -> ../../anaconda/bin/aws.cmd
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 aws_completer -> ../../anaconda/bin/aws_completer
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 aws_zsh_completer.sh -> ../../anaconda/bin/aws_zsh_completer.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 b2ct -> ../../anaconda/bin/b2ct
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 bam -> ../../anaconda/bin/bam
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 bam12auxmerge -> ../../anaconda/bin/bam12auxmerge
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bam12split -> ../../anaconda/bin/bam12split
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bam12strip -> ../../anaconda/bin/bam12strip
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 16:06 bam2fastx -> ../../anaconda/envs/python2/bin/bam2fastx
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 bam2mr -> ../../anaconda/bin/bam2mr
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bamadapterclip -> ../../anaconda/bin/bamadapterclip
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bamadapterfind -> ../../anaconda/bin/bamadapterfind
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bamalignfrac -> ../../anaconda/bin/bamalignfrac
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bamauxmerge -> ../../anaconda/bin/bamauxmerge
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bamauxsort -> ../../anaconda/bin/bamauxsort
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 bamcat -> ../../anaconda/bin/bamcat
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bamchecksort -> ../../anaconda/bin/bamchecksort
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bamclipreinsert -> ../../anaconda/bin/bamclipreinsert
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bamcollate -> ../../anaconda/bin/bamcollate
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bamcollate2 -> ../../anaconda/bin/bamcollate2
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bamCompare -> ../../anaconda/bin/bamCompare
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bamCoverage -> ../../anaconda/bin/bamCoverage
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 15:55 bamdownsamplerandom -> ../../anaconda/bin/bamdownsamplerandom
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 bamdump -> ../../anaconda/bin/bamdump
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bamexplode -> ../../anaconda/bin/bamexplode
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bamfillquery -> ../../anaconda/bin/bamfillquery
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bamfilteraux -> ../../anaconda/bin/bamfilteraux
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bamfilterflags -> ../../anaconda/bin/bamfilterflags
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bamfilterheader -> ../../anaconda/bin/bamfilterheader
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 bamfilterheader2 -> ../../anaconda/bin/bamfilterheader2
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bamfilterlength -> ../../anaconda/bin/bamfilterlength
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bamfiltermc -> ../../anaconda/bin/bamfiltermc
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bamfilternames -> ../../anaconda/bin/bamfilternames
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bamfilterrefid -> ../../anaconda/bin/bamfilterrefid
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bamfilterrg -> ../../anaconda/bin/bamfilterrg
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 15:55 bamfixmateinformation -> ../../anaconda/bin/bamfixmateinformation
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bamflagsplit -> ../../anaconda/bin/bamflagsplit
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bamheap2 -> ../../anaconda/bin/bamheap2
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bamindex -> ../../anaconda/bin/bamindex
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 bamintervalcomment -> ../../anaconda/bin/bamintervalcomment
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 15:55 bamintervalcommenthist -> ../../anaconda/bin/bamintervalcommenthist
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 bamlastfilter -> ../../anaconda/bin/bamlastfilter
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bamleftalign -> ../../anaconda/bin/bamleftalign
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bammapdist -> ../../anaconda/bin/bammapdist
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 bammarkduplicates -> ../../anaconda/bin/bammarkduplicates
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 bammarkduplicates2 -> ../../anaconda/bin/bammarkduplicates2
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 bammarkduplicatesopt -> ../../anaconda/bin/bammarkduplicatesopt
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bammaskflags -> ../../anaconda/bin/bammaskflags
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 bammdnm -> ../../anaconda/bin/bammdnm
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bammerge -> ../../anaconda/bin/bammerge
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 16:06 bam_merge -> ../../anaconda/envs/python2/bin/bam_merge
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 bamnumericalindex -> ../../anaconda/bin/bamnumericalindex
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 bamPEFragmentSize -> ../../anaconda/bin/bamPEFragmentSize
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 bamrank -> ../../anaconda/bin/bamrank
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bamranksort -> ../../anaconda/bin/bamranksort
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 15:55 bamrecalculatecigar -> ../../anaconda/bin/bamrecalculatecigar
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 bamrecompress -> ../../anaconda/bin/bamrecompress
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bamrefinterval -> ../../anaconda/bin/bamrefinterval
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bamreset -> ../../anaconda/bin/bamreset
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 bamscrapcount -> ../../anaconda/bin/bamscrapcount
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bamseqchksum -> ../../anaconda/bin/bamseqchksum
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bamsormadup -> ../../anaconda/bin/bamsormadup
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 bamsort -> ../../anaconda/bin/bamsort
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bamsplit -> ../../anaconda/bin/bamsplit
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bamsplitdiv -> ../../anaconda/bin/bamsplitdiv
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 16:06 bamstats.py -> ../../anaconda/envs/python2/bin/bamstats.py
lrwxrwxrwx 1 amizeranschi amizeranschi 45 Mar  3 15:55 bamstreamingmarkduplicates -> ../../anaconda/bin/bamstreamingmarkduplicates
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 bamtagconversion -> ../../anaconda/bin/bamtagconversion
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bamToBed -> ../../anaconda/bin/bamToBed
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bamtofastq -> ../../anaconda/bin/bamtofastq
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bamToFastq -> ../../anaconda/bin/bamToFastq
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bamToGBrowse.pl -> ../../anaconda/bin/bamToGBrowse.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bamtools -> ../../anaconda/bin/bamtools
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bamtools-2.4.0 -> ../../anaconda/bin/bamtools-2.4.0
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bamvalidate -> ../../anaconda/bin/bamvalidate
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bamzztoname -> ../../anaconda/bin/bamzztoname
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 15:55 battenberg_CN_to_VCF.pl -> ../../anaconda/bin/battenberg_CN_to_VCF.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 battenberg.pl -> ../../anaconda/bin/battenberg.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 15:55 battenberg_version.pl -> ../../anaconda/bin/battenberg_version.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bbcms.sh -> ../../anaconda/bin/bbcms.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 bbcountunique.sh -> ../../anaconda/bin/bbcountunique.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bbduk.sh -> ../../anaconda/bin/bbduk.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bbest.sh -> ../../anaconda/bin/bbest.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bbfakereads.sh -> ../../anaconda/bin/bbfakereads.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bbmap.sh -> ../../anaconda/bin/bbmap.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bbmapskimmer.sh -> ../../anaconda/bin/bbmapskimmer.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 bbmask.sh -> ../../anaconda/bin/bbmask.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bbmerge-auto.sh -> ../../anaconda/bin/bbmerge-auto.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bbmerge.sh -> ../../anaconda/bin/bbmerge.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 bbnorm.sh -> ../../anaconda/bin/bbnorm.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bbrealign.sh -> ../../anaconda/bin/bbrealign.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bbrename.sh -> ../../anaconda/bin/bbrename.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bbsketch.sh -> ../../anaconda/bin/bbsketch.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bbsplitpairs.sh -> ../../anaconda/bin/bbsplitpairs.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bbsplit.sh -> ../../anaconda/bin/bbsplit.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bbstats.sh -> ../../anaconda/bin/bbstats.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bbversion.sh -> ../../anaconda/bin/bbversion.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 bbwrap.sh -> ../../anaconda/bin/bbwrap.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 16:09 bcbio_conda -> ../../anaconda/bin/conda
lrwxrwxrwx 1 amizeranschi amizeranschi 91 Mar  3 15:26 bcbio_fastq_umi_prep.py -> /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/bin/bcbio_fastq_umi_prep.py
lrwxrwxrwx 1 amizeranschi amizeranschi 84 Mar  3 15:26 bcbio_nextgen.py -> /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/bin/bcbio_nextgen.py
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 16:09 bcbio_pip -> ../../anaconda/bin/pip
lrwxrwxrwx 1 amizeranschi amizeranschi 92 Mar  3 15:26 bcbio_prepare_samples.py -> /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/bin/bcbio_prepare_samples.py
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 bcbio-prioritize -> ../../anaconda/bin/bcbio-prioritize
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 16:09 bcbio_python -> ../../anaconda/bin/python
lrwxrwxrwx 1 amizeranschi amizeranschi 89 Mar  3 15:26 bcbio_setup_genome.py -> /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/bin/bcbio_setup_genome.py
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bcbio-variation -> ../../anaconda/bin/bcbio-variation
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 15:55 bcbio-variation-recall -> ../../anaconda/bin/bcbio-variation-recall
lrwxrwxrwx 1 amizeranschi amizeranschi 92 Mar  3 16:29 bcbio_vm.py -> /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/envs/bcbiovm/bin/bcbio_vm.py
lrwxrwxrwx 1 amizeranschi amizeranschi 87 Mar  3 16:29 bcbiovm_python -> /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/envs/bcbiovm/bin/python
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bcftools -> ../../anaconda/bin/bcftools
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bed12ToBed6 -> ../../anaconda/bin/bed12ToBed6
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bed2region -> ../../anaconda/bin/bed2region
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 bedGraphToBigWig -> ../../anaconda/bin/bedGraphToBigWig
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bedpeToBam -> ../../anaconda/bin/bedpeToBam
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bedToBam -> ../../anaconda/bin/bedToBam
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bedToBigBed -> ../../anaconda/bin/bedToBigBed
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bedToIgv -> ../../anaconda/bin/bedToIgv
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 16:06 bed_to_juncs -> ../../anaconda/envs/python2/bin/bed_to_juncs
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 bedtools -> ../../anaconda/bin/bedtools
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 bFst -> ../../anaconda/bin/bFst
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 bgzip -> ../../anaconda/bin/bgzip
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bgziptabix -> ../../anaconda/bin/bgziptabix
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bigBedInfo -> ../../anaconda/bin/bigBedInfo
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 bigBedSummary -> ../../anaconda/bin/bigBedSummary
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bigBedToBed -> ../../anaconda/bin/bigBedToBed
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 bigwigCompare -> ../../anaconda/bin/bigwigCompare
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 bigWigInfo -> ../../anaconda/bin/bigWigInfo
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 bigWigSummary -> ../../anaconda/bin/bigWigSummary
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 bigWigToBedGraph -> ../../anaconda/bin/bigWigToBedGraph
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 bigWigToWig -> ../../anaconda/bin/bigWigToWig
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 bio-vcf -> ../../anaconda/bin/bio-vcf
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 blast2sam.pl -> ../../anaconda/bin/blast2sam.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 16:06 blocksplit -> ../../anaconda/envs/python2/bin/blocksplit
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bloomfilter.sh -> ../../anaconda/bin/bloomfilter.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 bowtie -> ../../anaconda/bin/bowtie
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 bowtie2 -> ../../anaconda/bin/bowtie2
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bowtie2-align-l -> ../../anaconda/bin/bowtie2-align-l
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bowtie2-align-s -> ../../anaconda/bin/bowtie2-align-s
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 bowtie2-build -> ../../anaconda/bin/bowtie2-build
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bowtie2-build-l -> ../../anaconda/bin/bowtie2-build-l
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bowtie2-build-s -> ../../anaconda/bin/bowtie2-build-s
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 bowtie2-inspect -> ../../anaconda/bin/bowtie2-inspect
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 bowtie2-inspect-l -> ../../anaconda/bin/bowtie2-inspect-l
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 bowtie2-inspect-s -> ../../anaconda/bin/bowtie2-inspect-s
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 bowtie2sam.pl -> ../../anaconda/bin/bowtie2sam.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bowtie-align-l -> ../../anaconda/bin/bowtie-align-l
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bowtie-align-s -> ../../anaconda/bin/bowtie-align-s
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bowtie-build -> ../../anaconda/bin/bowtie-build
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bowtie-build-l -> ../../anaconda/bin/bowtie-build-l
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bowtie-build-s -> ../../anaconda/bin/bowtie-build-s
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 bowtie-inspect -> ../../anaconda/bin/bowtie-inspect
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 bowtie-inspect-l -> ../../anaconda/bin/bowtie-inspect-l
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 bowtie-inspect-s -> ../../anaconda/bin/bowtie-inspect-s
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 15:55 break-point-inspector -> ../../anaconda/bin/break-point-inspector
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 bunzip2 -> ../../anaconda/bin/bunzip2
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 bwa -> ../../anaconda/bin/bwa
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 bzcat -> ../../anaconda/bin/bzcat
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 bzcmp -> ../../anaconda/bin/bzcmp
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 bzdiff -> ../../anaconda/bin/bzdiff
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 bzegrep -> ../../anaconda/bin/bzegrep
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 bzfgrep -> ../../anaconda/bin/bzfgrep
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 bzgrep -> ../../anaconda/bin/bzgrep
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 bzip2 -> ../../anaconda/bin/bzip2
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 bzip2recover -> ../../anaconda/bin/bzip2recover
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 bzless -> ../../anaconda/bin/bzless
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 bzmore -> ../../anaconda/bin/bzmore
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 cage -> ../../anaconda/bin/cage
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 cage-classify.py -> ../../anaconda/bin/cage-classify.py
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 calcmem.sh -> ../../anaconda/bin/calcmem.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 calctruequality.sh -> ../../anaconda/bin/calctruequality.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 callpeaks.sh -> ../../anaconda/bin/callpeaks.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 callvariants2.sh -> ../../anaconda/bin/callvariants2.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 callvariants.sh -> ../../anaconda/bin/callvariants.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 captoinfo -> ../../anaconda/bin/captoinfo
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 cbc -> ../../anaconda/bin/cbc
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 chipseq-greylist -> ../../anaconda/bin/chipseq-greylist
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 chrom_sizes.pl -> ../../anaconda/bin/chrom_sizes.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 chronic -> ../../anaconda/bin/chronic
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 clear -> ../../anaconda/bin/clear
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 closestBed -> ../../anaconda/bin/closestBed
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 clp -> ../../anaconda/bin/clp
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 clumpify.sh -> ../../anaconda/bin/clumpify.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 clusterBed -> ../../anaconda/bin/clusterBed
lrwxrwxrwx 1 amizeranschi amizeranschi 54 Mar  3 16:06 cnvanator_to_bedpes.py -> ../../anaconda/envs/python2/bin/cnvanator_to_bedpes.py
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 cnv_annotate.py -> ../../anaconda/bin/cnv_annotate.py
lrwxrwxrwx 1 amizeranschi amizeranschi 46 Mar  3 15:55 cnv_expression_correlate.py -> ../../anaconda/bin/cnv_expression_correlate.py
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 cnvkit.py -> ../../anaconda/bin/cnvkit.py
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 cnv_updater.py -> ../../anaconda/bin/cnv_updater.py
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 cnv_ztest.py -> ../../anaconda/bin/cnv_ztest.py
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 16:06 cnx.py -> ../../anaconda/envs/python2/bin/cnx.py
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 COBALT -> ../../anaconda/bin/COBALT
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 color-chrs.pl -> ../../anaconda/bin/color-chrs.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 combine -> ../../anaconda/bin/combine
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 commonkmers.sh -> ../../anaconda/bin/commonkmers.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 comparesketch.sh -> ../../anaconda/bin/comparesketch.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 comparevcf.sh -> ../../anaconda/bin/comparevcf.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 complementBed -> ../../anaconda/bin/complementBed
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 computeGCBias -> ../../anaconda/bin/computeGCBias
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 computeMatrix -> ../../anaconda/bin/computeMatrix
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 15:55 computeMatrixOperations -> ../../anaconda/bin/computeMatrixOperations
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 conda_build.sh -> ../../anaconda/bin/conda_build.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 46 Mar  3 16:06 configManta.py -> ../../anaconda/envs/python2/bin/configManta.py
lrwxrwxrwx 1 amizeranschi amizeranschi 67 Mar  3 16:06 configureStrelkaGermlineWorkflow.py -> ../../anaconda/envs/python2/bin/configureStrelkaGermlineWorkflow.py
lrwxrwxrwx 1 amizeranschi amizeranschi 66 Mar  3 16:06 configureStrelkaSomaticWorkflow.py -> ../../anaconda/envs/python2/bin/configureStrelkaSomaticWorkflow.py
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 consect.sh -> ../../anaconda/bin/consect.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 52 Mar  3 16:06 contig_to_chr_coords -> ../../anaconda/envs/python2/bin/contig_to_chr_coords
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 correctGCBias -> ../../anaconda/bin/correctGCBias
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 countbarcodes.sh -> ../../anaconda/bin/countbarcodes.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 countgc.sh -> ../../anaconda/bin/countgc.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 15:55 countsharedlines.sh -> ../../anaconda/bin/countsharedlines.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 cov2lr.pl -> ../../anaconda/bin/cov2lr.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 coverageBed -> ../../anaconda/bin/coverageBed
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 15:55 coverage_to_regions.py -> ../../anaconda/bin/coverage_to_regions.py
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 cpanm -> ../../anaconda/bin/cpanm
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 16:06 cpat.py -> ../../anaconda/envs/python2/bin/cpat.py
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 cramtools -> ../../anaconda/bin/cramtools
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 crc32 -> ../../anaconda/bin/crc32
lrwxrwxrwx 1 amizeranschi amizeranschi 50 Mar  3 16:06 create_coordinates -> ../../anaconda/envs/python2/bin/create_coordinates
lrwxrwxrwx 1 amizeranschi amizeranschi 57 Mar  3 16:06 create_phylowgs_inputs.py -> ../../anaconda/envs/python2/bin/create_phylowgs_inputs.py
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 crossblock.sh -> ../../anaconda/bin/crossblock.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 15:55 crosscontaminate.sh -> ../../anaconda/bin/crosscontaminate.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 16:08 CrossMap.py -> ../../anaconda/envs/python3/bin/CrossMap.py
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 ct2db -> ../../anaconda/bin/ct2db
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 cuffcompare -> ../../anaconda/bin/cuffcompare
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 cuffdiff -> ../../anaconda/bin/cuffdiff
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 cufflinks -> ../../anaconda/bin/cufflinks
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 cuffmerge -> ../../anaconda/bin/cuffmerge
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 cuffnorm -> ../../anaconda/bin/cuffnorm
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 cuffquant -> ../../anaconda/bin/cuffquant
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 16:06 cutadapt -> ../../anaconda/envs/python2/bin/cutadapt
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 cutprimers.sh -> ../../anaconda/bin/cutprimers.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 cyvcf2 -> ../../anaconda/bin/cyvcf2
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 dbilogstrip -> ../../anaconda/bin/dbilogstrip
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 dbiprof -> ../../anaconda/bin/dbiprof
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 dbiproxy -> ../../anaconda/bin/dbiproxy
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 decontaminate.sh -> ../../anaconda/bin/decontaminate.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 dedupe2.sh -> ../../anaconda/bin/dedupe2.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 dedupebymapping.sh -> ../../anaconda/bin/dedupebymapping.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 dedupe.sh -> ../../anaconda/bin/dedupe.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 deeptools -> ../../anaconda/bin/deeptools
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 delly -> ../../anaconda/bin/delly
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 demuxbyname.sh -> ../../anaconda/bin/demuxbyname.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 detectionCall -> ../../anaconda/bin/detectionCall
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 dexseq_count.py -> ../../anaconda/bin/dexseq_count.py
lrwxrwxrwx 1 amizeranschi amizeranschi 47 Mar  3 15:55 dexseq_prepare_annotation.py -> ../../anaconda/bin/dexseq_prepare_annotation.py
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 16:06 dipenum -> ../../anaconda/envs/python2/bin/dipenum
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 diskbench.sh -> ../../anaconda/bin/diskbench.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 49 Mar  3 16:06 dkfzbiasfilter.py -> ../../anaconda/envs/python2/bin/dkfzbiasfilter.py
lrwxrwxrwx 1 amizeranschi amizeranschi 59 Mar  3 16:06 dkfzbiasfilter_summarize.py -> ../../anaconda/envs/python2/bin/dkfzbiasfilter_summarize.py
lrwxrwxrwx 1 amizeranschi amizeranschi 55 Mar  3 15:55 download_generate_bberg_ref_files.pl -> ../../anaconda/bin/download_generate_bberg_ref_files.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 15:55 dumpContigsFromHeader -> ../../anaconda/bin/dumpContigsFromHeader
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 duphold -> ../../anaconda/bin/duphold
lrwxrwxrwx 1 amizeranschi amizeranschi 46 Mar  3 16:00 dv_call_variants.py -> ../../anaconda/envs/dv/bin/dv_call_variants.py
lrwxrwxrwx 1 amizeranschi amizeranschi 46 Mar  3 16:00 dv_make_examples.py -> ../../anaconda/envs/dv/bin/dv_make_examples.py
lrwxrwxrwx 1 amizeranschi amizeranschi 53 Mar  3 16:00 dv_postprocess_variants.py -> ../../anaconda/envs/dv/bin/dv_postprocess_variants.py
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 env_parallel -> ../../anaconda/bin/env_parallel
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 env_parallel.ash -> ../../anaconda/bin/env_parallel.ash
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 env_parallel.bash -> ../../anaconda/bin/env_parallel.bash
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 env_parallel.csh -> ../../anaconda/bin/env_parallel.csh
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 env_parallel.dash -> ../../anaconda/bin/env_parallel.dash
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 env_parallel.fish -> ../../anaconda/bin/env_parallel.fish
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 env_parallel.ksh -> ../../anaconda/bin/env_parallel.ksh
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 env_parallel.mksh -> ../../anaconda/bin/env_parallel.mksh
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 env_parallel.pdksh -> ../../anaconda/bin/env_parallel.pdksh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 env_parallel.sh -> ../../anaconda/bin/env_parallel.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 env_parallel.tcsh -> ../../anaconda/bin/env_parallel.tcsh
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 env_parallel.zsh -> ../../anaconda/bin/env_parallel.zsh
lrwxrwxrwx 1 amizeranschi amizeranschi 47 Mar  3 16:09 ericscript.pl -> ../../anaconda/envs/samtools0/bin/ericscript.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 errno -> ../../anaconda/bin/errno
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 estherfilter.sh -> ../../anaconda/bin/estherfilter.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 15:55 estimateReadFiltering -> ../../anaconda/bin/estimateReadFiltering
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 15:55 estimateScaleFactor -> ../../anaconda/bin/estimateScaleFactor
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 16:06 evolve.py -> ../../anaconda/envs/python2/bin/evolve.py
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 exactSNP -> ../../anaconda/bin/exactSNP
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 example -> ../../anaconda/bin/example
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 expandCols -> ../../anaconda/bin/expandCols
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 explodetree.sh -> ../../anaconda/bin/explodetree.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 export2sam.pl -> ../../anaconda/bin/export2sam.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 express -> ../../anaconda/bin/express
lrwxrwxrwx 1 amizeranschi amizeranschi 56 Mar  3 16:06 extractSplitReads_BwaMem -> ../../anaconda/envs/python2/bin/extractSplitReads_BwaMem
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 extract-sv-reads -> ../../anaconda/bin/extract-sv-reads
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 fastaFromBed -> ../../anaconda/bin/fastaFromBed
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 15:55 fasta_generate_regions.py -> ../../anaconda/bin/fasta_generate_regions.py
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 16:06 fastainfo -> ../../anaconda/envs/python2/bin/fastainfo
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 fastp -> ../../anaconda/bin/fastp
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 fastqc -> ../../anaconda/bin/fastqc
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 faToTwoBit -> ../../anaconda/bin/faToTwoBit
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 featureCounts -> ../../anaconda/bin/featureCounts
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 fgbio -> ../../anaconda/bin/fgbio
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 15:55 filterassemblysummary.sh -> ../../anaconda/bin/filterassemblysummary.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 filterbarcodes.sh -> ../../anaconda/bin/filterbarcodes.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 15:55 filterbycoverage.sh -> ../../anaconda/bin/filterbycoverage.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 filterbyname.sh -> ../../anaconda/bin/filterbyname.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 15:55 filterbysequence.sh -> ../../anaconda/bin/filterbysequence.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 filterbytaxa.sh -> ../../anaconda/bin/filterbytaxa.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 filterbytile.sh -> ../../anaconda/bin/filterbytile.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 filterlines.sh -> ../../anaconda/bin/filterlines.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 filterqc.sh -> ../../anaconda/bin/filterqc.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 filtersam.sh -> ../../anaconda/bin/filtersam.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 filtersubs.sh -> ../../anaconda/bin/filtersubs.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 filtervcf.sh -> ../../anaconda/bin/filtervcf.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 filter_vep -> ../../anaconda/bin/filter_vep
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 find_pycompletion.sh -> ../../anaconda/bin/find_pycompletion.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 48 Mar  3 16:06 fix_map_ordering -> ../../anaconda/envs/python2/bin/fix_map_ordering
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 flankBed -> ../../anaconda/bin/flankBed
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 flattenGTF -> ../../anaconda/bin/flattenGTF
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 freebayes -> ../../anaconda/bin/freebayes
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 freebayes-parallel -> ../../anaconda/bin/freebayes-parallel
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 16:06 ftx.py -> ../../anaconda/envs/python2/bin/ftx.py
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 fungalrelease.sh -> ../../anaconda/bin/fungalrelease.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 fuse.sh -> ../../anaconda/bin/fuse.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 gatk -> ../../anaconda/bin/gatk
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 gatk3 -> ../../anaconda/bin/gatk3
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 gatk3-register -> ../../anaconda/bin/gatk3-register
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 16:06 gemini -> ../../anaconda/envs/python2/bin/gemini
lrwxrwxrwx 1 amizeranschi amizeranschi 55 Mar  3 15:55 generate_freebayes_region_scripts.sh -> ../../anaconda/bin/generate_freebayes_region_scripts.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 genesplicer -> ../../anaconda/bin/genesplicer
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 GenomeAnalysisTK -> ../../anaconda/bin/GenomeAnalysisTK
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 genomeCoverageBed -> ../../anaconda/bin/genomeCoverageBed
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 genomeCoverageBed.pl -> ../../anaconda/bin/genomeCoverageBed.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 genotypeSummary -> ../../anaconda/bin/genotypeSummary
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 getOverlap -> ../../anaconda/bin/getOverlap
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 getreads.sh -> ../../anaconda/bin/getreads.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 gffcompare -> ../../anaconda/bin/gffcompare
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 gffread -> ../../anaconda/bin/gffread
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 gi2ancestors.sh -> ../../anaconda/bin/gi2ancestors.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 gi2taxid.sh -> ../../anaconda/bin/gi2taxid.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 gitable.sh -> ../../anaconda/bin/gitable.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 gof3r -> ../../anaconda/bin/gof3r
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 goleft -> ../../anaconda/bin/goleft
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 grabix -> ../../anaconda/bin/grabix
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 grademerge.sh -> ../../anaconda/bin/grademerge.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 gradesam.sh -> ../../anaconda/bin/gradesam.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 gridss -> ../../anaconda/bin/gridss
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 groupBy -> ../../anaconda/bin/groupBy
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 gsort -> ../../anaconda/bin/gsort
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 16:06 gtf_juncs -> ../../anaconda/envs/python2/bin/gtf_juncs
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 16:06 gtf_to_fasta -> ../../anaconda/envs/python2/bin/gtf_to_fasta
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 gtfToGenePred -> ../../anaconda/bin/gtfToGenePred
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 gtf_to_sam -> ../../anaconda/bin/gtf_to_sam
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 guess_baits.py -> ../../anaconda/bin/guess_baits.py
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 guess-ploidy.py -> ../../anaconda/bin/guess-ploidy.py
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 16:06 gvcf2bed -> ../../anaconda/envs/python2/bin/gvcf2bed
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 gvcfgenotyper -> ../../anaconda/bin/gvcfgenotyper
lrwxrwxrwx 1 amizeranschi amizeranschi 47 Mar  3 16:06 gvcf_regions.py -> ../../anaconda/envs/python2/bin/gvcf_regions.py
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 16:06 hapcmp -> ../../anaconda/envs/python2/bin/hapcmp
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 16:06 hapenum -> ../../anaconda/envs/python2/bin/hapenum
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 haplo -> ../../anaconda/bin/haplo
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 hapLrt -> ../../anaconda/bin/hapLrt
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 16:06 hap.py -> ../../anaconda/envs/python2/bin/hap.py
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 hisat2 -> ../../anaconda/bin/hisat2
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 hisat2-align-l -> ../../anaconda/bin/hisat2-align-l
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 hisat2-align-s -> ../../anaconda/bin/hisat2-align-s
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 hisat2-build -> ../../anaconda/bin/hisat2-build
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 hisat2-build-l -> ../../anaconda/bin/hisat2-build-l
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 hisat2-build-s -> ../../anaconda/bin/hisat2-build-s
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 15:55 hisat2_extract_exons.py -> ../../anaconda/bin/hisat2_extract_exons.py
lrwxrwxrwx 1 amizeranschi amizeranschi 57 Mar  3 15:55 hisat2_extract_snps_haplotypes_UCSC.py -> ../../anaconda/bin/hisat2_extract_snps_haplotypes_UCSC.py
lrwxrwxrwx 1 amizeranschi amizeranschi 56 Mar  3 15:55 hisat2_extract_snps_haplotypes_VCF.py -> ../../anaconda/bin/hisat2_extract_snps_haplotypes_VCF.py
lrwxrwxrwx 1 amizeranschi amizeranschi 49 Mar  3 15:55 hisat2_extract_splice_sites.py -> ../../anaconda/bin/hisat2_extract_splice_sites.py
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 hisat2-inspect -> ../../anaconda/bin/hisat2-inspect
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 hisat2-inspect-l -> ../../anaconda/bin/hisat2-inspect-l
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 hisat2-inspect-s -> ../../anaconda/bin/hisat2-inspect-s
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 15:55 hisat2_simulate_reads.py -> ../../anaconda/bin/hisat2_simulate_reads.py
lrwxrwxrwx 1 amizeranschi amizeranschi 48 Mar  3 15:55 hisatgenotype_build_genome.py -> ../../anaconda/bin/hisatgenotype_build_genome.py
lrwxrwxrwx 1 amizeranschi amizeranschi 49 Mar  3 15:55 hisatgenotype_extract_reads.py -> ../../anaconda/bin/hisatgenotype_extract_reads.py
lrwxrwxrwx 1 amizeranschi amizeranschi 48 Mar  3 15:55 hisatgenotype_extract_vars.py -> ../../anaconda/bin/hisatgenotype_extract_vars.py
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 15:55 hisatgenotype_hla_cyp.py -> ../../anaconda/bin/hisatgenotype_hla_cyp.py
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 15:55 hisatgenotype_locus.py -> ../../anaconda/bin/hisatgenotype_locus.py
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 hisatgenotype.py -> ../../anaconda/bin/hisatgenotype.py
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 htseq-count -> ../../anaconda/bin/htseq-count
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 htseq-qa -> ../../anaconda/bin/htseq-qa
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 htsfile -> ../../anaconda/bin/htsfile
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 hts_nim_tools -> ../../anaconda/bin/hts_nim_tools
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 idmatrix.sh -> ../../anaconda/bin/idmatrix.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 idtree.sh -> ../../anaconda/bin/idtree.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 ifdata -> ../../anaconda/bin/ifdata
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 ifne -> ../../anaconda/bin/ifne
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 iHS -> ../../anaconda/bin/iHS
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 impute2 -> ../../anaconda/bin/impute2
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 infocmp -> ../../anaconda/bin/infocmp
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 infotocap -> ../../anaconda/bin/infotocap
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 installpackages.R -> ../../anaconda/bin/installpackages.R
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 interpolate_sam.pl -> ../../anaconda/bin/interpolate_sam.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 intersectBed -> ../../anaconda/bin/intersectBed
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 16:06 intervaltree -> ../../anaconda/envs/python2/bin/intervaltree
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 invertkey.sh -> ../../anaconda/bin/invertkey.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 IONTorrent.R -> ../../anaconda/bin/IONTorrent.R
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 isnovoindex -> ../../anaconda/bin/isnovoindex
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 isutf8 -> ../../anaconda/bin/isutf8
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 16:06 juncs_db -> ../../anaconda/envs/python2/bin/juncs_db
lrwxrwxrwx 1 amizeranschi amizeranschi 21 Mar  3 15:55 k8 -> ../../anaconda/bin/k8
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 kallisto -> ../../anaconda/bin/kallisto
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 kcompress.sh -> ../../anaconda/bin/kcompress.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 khist.sh -> ../../anaconda/bin/khist.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 Kinfold -> ../../anaconda/bin/Kinfold
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 kinwalker -> ../../anaconda/bin/kinwalker
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 kmercountexact.sh -> ../../anaconda/bin/kmercountexact.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 kmercountmulti.sh -> ../../anaconda/bin/kmercountmulti.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 kmercoverage.sh -> ../../anaconda/bin/kmercoverage.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 kmerlimit2.sh -> ../../anaconda/bin/kmerlimit2.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 kmerlimit.sh -> ../../anaconda/bin/kmerlimit.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 kraken -> ../../anaconda/bin/kraken
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 kraken-build -> ../../anaconda/bin/kraken-build
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 kraken-filter -> ../../anaconda/bin/kraken-filter
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 kraken-mpa-report -> ../../anaconda/bin/kraken-mpa-report
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 kraken-report -> ../../anaconda/bin/kraken-report
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 kraken-translate -> ../../anaconda/bin/kraken-translate
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 lckdo -> ../../anaconda/bin/lckdo
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 16:06 lib_stats.R -> ../../anaconda/envs/python2/bin/lib_stats.R
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 liftOver -> ../../anaconda/bin/liftOver
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 linksBed -> ../../anaconda/bin/linksBed
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 loadreads.sh -> ../../anaconda/bin/loadreads.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 lofreq -> ../../anaconda/bin/lofreq
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 15:55 lofreq2_call_pparallel.py -> ../../anaconda/bin/lofreq2_call_pparallel.py
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 lofreq2_somatic.py -> ../../anaconda/bin/lofreq2_somatic.py
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 loglog.sh -> ../../anaconda/bin/loglog.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 51 Mar  3 16:06 long_spanning_reads -> ../../anaconda/envs/python2/bin/long_spanning_reads
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 lr2gene.pl -> ../../anaconda/bin/lr2gene.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 16:06 lumpy -> ../../anaconda/envs/python2/bin/lumpy
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 16:06 lumpyexpress -> ../../anaconda/envs/python2/bin/lumpyexpress
lrwxrwxrwx 1 amizeranschi amizeranschi 51 Mar  3 16:06 lumpyexpress.config -> ../../anaconda/envs/python2/bin/lumpyexpress.config
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 16:06 lumpy_filter -> ../../anaconda/envs/python2/bin/lumpy_filter
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 lwp-download -> ../../anaconda/bin/lwp-download
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 lwp-dump -> ../../anaconda/bin/lwp-dump
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 lwp-mirror -> ../../anaconda/bin/lwp-mirror
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 lwp-request -> ../../anaconda/bin/lwp-request
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 lzcat -> ../../anaconda/bin/lzcat
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 lzcmp -> ../../anaconda/bin/lzcmp
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 lzdiff -> ../../anaconda/bin/lzdiff
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 lzegrep -> ../../anaconda/bin/lzegrep
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 lzfgrep -> ../../anaconda/bin/lzfgrep
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 lzgrep -> ../../anaconda/bin/lzgrep
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 lzless -> ../../anaconda/bin/lzless
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 lzma -> ../../anaconda/bin/lzma
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 lzmadec -> ../../anaconda/bin/lzmadec
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 lzmainfo -> ../../anaconda/bin/lzmainfo
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 lzmore -> ../../anaconda/bin/lzmore
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 16:06 macs2 -> ../../anaconda/envs/python2/bin/macs2
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 makechimeras.sh -> ../../anaconda/bin/makechimeras.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 45 Mar  3 15:55 makecontaminatedgenomes.sh -> ../../anaconda/bin/makecontaminatedgenomes.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 51 Mar  3 16:06 make_hexamer_tab.py -> ../../anaconda/envs/python2/bin/make_hexamer_tab.py
lrwxrwxrwx 1 amizeranschi amizeranschi 50 Mar  3 16:06 make_logitModel.py -> ../../anaconda/envs/python2/bin/make_logitModel.py
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 makepolymers.sh -> ../../anaconda/bin/makepolymers.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 16:06 map2gtf -> ../../anaconda/envs/python2/bin/map2gtf
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 mapBed -> ../../anaconda/bin/mapBed
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 mapPacBio.sh -> ../../anaconda/bin/mapPacBio.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 maq2sam-long -> ../../anaconda/bin/maq2sam-long
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 maq2sam-short -> ../../anaconda/bin/maq2sam-short
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 maskFastaFromBed -> ../../anaconda/bin/maskFastaFromBed
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 matrixtocolumns.sh -> ../../anaconda/bin/matrixtocolumns.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 maxentscan_score3.pl -> ../../anaconda/bin/maxentscan_score3.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 maxentscan_score5.pl -> ../../anaconda/bin/maxentscan_score5.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 mbuffer -> ../../anaconda/bin/mbuffer
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 md5fa -> ../../anaconda/bin/md5fa
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 md5sum-lite -> ../../anaconda/bin/md5sum-lite
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 meltEHH -> ../../anaconda/bin/meltEHH
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 mergebarcodes.sh -> ../../anaconda/bin/mergebarcodes.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 mergeBed -> ../../anaconda/bin/mergeBed
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 mergeOTUs.sh -> ../../anaconda/bin/mergeOTUs.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 mergesam.sh -> ../../anaconda/bin/mergesam.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 mergesketch.sh -> ../../anaconda/bin/mergesketch.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 mergesorted.sh -> ../../anaconda/bin/mergesorted.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 metaspades.py -> ../../anaconda/bin/metaspades.py
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 minimap2 -> ../../anaconda/bin/minimap2
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 MINTmap.pl -> ../../anaconda/bin/MINTmap.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 miraligner -> ../../anaconda/bin/miraligner
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 miRDeep2.pl -> ../../anaconda/bin/miRDeep2.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 16:06 miRge2.0 -> ../../anaconda/envs/python2/bin/miRge2.0
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 mirtop -> ../../anaconda/bin/mirtop
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 mispipe -> ../../anaconda/bin/mispipe
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 modules -> ../../anaconda/bin/modules
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 mosdepth -> ../../anaconda/bin/mosdepth
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 msa.sh -> ../../anaconda/bin/msa.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 multiBamCov -> ../../anaconda/bin/multiBamCov
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 multiBamSummary -> ../../anaconda/bin/multiBamSummary
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 multiBigwigSummary -> ../../anaconda/bin/multiBigwigSummary
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 multiIntersectBed -> ../../anaconda/bin/multiIntersectBed
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 16:06 multimerge -> ../../anaconda/envs/python2/bin/multimerge
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 multiqc -> ../../anaconda/bin/multiqc
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 mutate.sh -> ../../anaconda/bin/mutate.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 muxbyname.sh -> ../../anaconda/bin/muxbyname.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 ncurses6-config -> ../../anaconda/bin/ncurses6-config
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 ncursesw6-config -> ../../anaconda/bin/ncursesw6-config
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 ngs_disambiguate -> ../../anaconda/bin/ngs_disambiguate
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 niceload -> ../../anaconda/bin/niceload
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 node -> ../../anaconda/bin/node
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 normalize-iHS -> ../../anaconda/bin/normalize-iHS
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 15:55 normandcorrectwrapper.sh -> ../../anaconda/bin/normandcorrectwrapper.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 novo2maq -> ../../anaconda/bin/novo2maq
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 novo2paf -> ../../anaconda/bin/novo2paf
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 novo2sam.pl -> ../../anaconda/bin/novo2sam.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 novoalign -> ../../anaconda/bin/novoalign
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 novoalignCS -> ../../anaconda/bin/novoalignCS
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 novoalignCSMPI -> ../../anaconda/bin/novoalignCSMPI
lrwxrwxrwx 1 amizeranschi amizeranschi 45 Mar  3 15:55 novoalign-license-register -> ../../anaconda/bin/novoalign-license-register
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 novoalignMPI -> ../../anaconda/bin/novoalignMPI
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 novobarcode -> ../../anaconda/bin/novobarcode
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 novoindex -> ../../anaconda/bin/novoindex
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 novolrcleaver -> ../../anaconda/bin/novolrcleaver
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 novolrcorrector -> ../../anaconda/bin/novolrcorrector
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 novolrpolish -> ../../anaconda/bin/novolrpolish
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 novomethyl -> ../../anaconda/bin/novomethyl
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 novope2bed.pl -> ../../anaconda/bin/novope2bed.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 novorun.pl -> ../../anaconda/bin/novorun.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 novosort -> ../../anaconda/bin/novosort
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 novoutil -> ../../anaconda/bin/novoutil
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 npm -> ../../anaconda/bin/npm
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 npx -> ../../anaconda/bin/npx
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 nucBed -> ../../anaconda/bin/nucBed
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 octopus -> ../../anaconda/bin/octopus
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 oncofuse -> ../../anaconda/bin/oncofuse
lrwxrwxrwx 1 amizeranschi amizeranschi 51 Mar  3 16:06 OptiTypePipeline.py -> ../../anaconda/envs/python2/bin/OptiTypePipeline.py
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 16:06 ovc.py -> ../../anaconda/envs/python2/bin/ovc.py
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 paftools.js -> ../../anaconda/bin/paftools.js
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 pairToBed -> ../../anaconda/bin/pairToBed
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 pairToPair -> ../../anaconda/bin/pairToPair
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 parallel -> ../../anaconda/bin/parallel
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 parcat -> ../../anaconda/bin/parcat
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 parset -> ../../anaconda/bin/parset
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 partition.sh -> ../../anaconda/bin/partition.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 pbgzip -> ../../anaconda/bin/pbgzip
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 16:06 peddy -> ../../anaconda/envs/python2/bin/peddy
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 pee -> ../../anaconda/bin/pee
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 permuteGPAT++ -> ../../anaconda/bin/permuteGPAT++
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 permuteSmooth -> ../../anaconda/bin/permuteSmooth
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 pFst -> ../../anaconda/bin/pFst
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 phylip2fasta.sh -> ../../anaconda/bin/phylip2fasta.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 picard -> ../../anaconda/bin/picard
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 pileup.sh -> ../../anaconda/bin/pileup.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 pindel -> ../../anaconda/bin/pindel
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 pindel2vcf -> ../../anaconda/bin/pindel2vcf
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 pindel2vcf4tcga -> ../../anaconda/bin/pindel2vcf4tcga
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 pizzly -> ../../anaconda/bin/pizzly
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 15:55 pizzly_flatten_json.py -> ../../anaconda/bin/pizzly_flatten_json.py
lrwxrwxrwx 1 amizeranschi amizeranschi 45 Mar  3 15:55 pizzly_flatten_json.py.bak -> ../../anaconda/bin/pizzly_flatten_json.py.bak
lrwxrwxrwx 1 amizeranschi amizeranschi 48 Mar  3 15:55 pizzly_get_fragment_length.py -> ../../anaconda/bin/pizzly_get_fragment_length.py
lrwxrwxrwx 1 amizeranschi amizeranschi 52 Mar  3 15:55 pizzly_get_fragment_length.py.bak -> ../../anaconda/bin/pizzly_get_fragment_length.py.bak
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 plasmidspades.py -> ../../anaconda/bin/plasmidspades.py
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 16:06 platypus -> ../../anaconda/envs/python2/bin/platypus
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 plot-bamstats -> ../../anaconda/bin/plot-bamstats
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 plotBfst.R -> ../../anaconda/bin/plotBfst.R
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 plotCorrelation -> ../../anaconda/bin/plotCorrelation
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 plotCoverage -> ../../anaconda/bin/plotCoverage
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 plotEnrichment -> ../../anaconda/bin/plotEnrichment
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 plotFingerprint -> ../../anaconda/bin/plotFingerprint
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 plotflowcell.sh -> ../../anaconda/bin/plotflowcell.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 plotgc.sh -> ../../anaconda/bin/plotgc.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 plotHaplotypes.R -> ../../anaconda/bin/plotHaplotypes.R
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 plotHapLrt.R -> ../../anaconda/bin/plotHapLrt.R
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 plotHaps -> ../../anaconda/bin/plotHaps
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 plotHeatmap -> ../../anaconda/bin/plotHeatmap
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 plotPCA -> ../../anaconda/bin/plotPCA
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 plotPfst.R -> ../../anaconda/bin/plotPfst.R
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 plotProfile -> ../../anaconda/bin/plotProfile
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 plot_roc.r -> ../../anaconda/bin/plot_roc.r
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 plot-roh.py -> ../../anaconda/bin/plot-roh.py
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 plotSmoothed.R -> ../../anaconda/bin/plotSmoothed.R
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 plot-vcfstats -> ../../anaconda/bin/plot-vcfstats
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 plotWCfst.R -> ../../anaconda/bin/plotWCfst.R
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 plotXPEHH.R -> ../../anaconda/bin/plotXPEHH.R
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 popStats -> ../../anaconda/bin/popStats
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 popt -> ../../anaconda/bin/popt
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 postfilter.sh -> ../../anaconda/bin/postfilter.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 prepDE.py -> ../../anaconda/bin/prepDE.py
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 16:06 prep_reads -> ../../anaconda/envs/python2/bin/prep_reads
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 16:06 preprocess -> ../../anaconda/envs/python2/bin/preprocess
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 16:06 pre.py -> ../../anaconda/envs/python2/bin/pre.py
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 preseq -> ../../anaconda/bin/preseq
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 printtime.sh -> ../../anaconda/bin/printtime.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 processfrag.sh -> ../../anaconda/bin/processfrag.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 processhi-c.sh -> ../../anaconda/bin/processhi-c.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 processspeed.sh -> ../../anaconda/bin/processspeed.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 propmapped -> ../../anaconda/bin/propmapped
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 psl2sam.pl -> ../../anaconda/bin/psl2sam.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 PURPLE -> ../../anaconda/bin/PURPLE
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 pVst -> ../../anaconda/bin/pVst
lrwxrwxrwx 1 amizeranschi amizeranschi 21 Mar  3 15:55 py -> ../../anaconda/bin/py
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 py2 -> ../../anaconda/bin/py2
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 py2.7 -> ../../anaconda/bin/py2.7
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 pycompleter -> ../../anaconda/bin/pycompleter
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 pycompleter2 -> ../../anaconda/bin/pycompleter2
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 pycompleter2.7 -> ../../anaconda/bin/pycompleter2.7
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 PyLOH.py -> ../../anaconda/bin/PyLOH.py
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 qcalplot.R -> ../../anaconda/bin/qcalplot.R
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 16:06 qfy.py -> ../../anaconda/envs/python2/bin/qfy.py
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 qsignature -> ../../anaconda/bin/qsignature
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 qualfa2fq.pl -> ../../anaconda/bin/qualfa2fq.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 qualimap -> ../../anaconda/bin/qualimap
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 qualityScores -> ../../anaconda/bin/qualityScores
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 16:06 quantify -> ../../anaconda/envs/python2/bin/quantify
lrwxrwxrwx 1 amizeranschi amizeranschi 20 Mar  3 15:55 R -> ../../anaconda/bin/R
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 randomBed -> ../../anaconda/bin/randomBed
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 randomgenome.sh -> ../../anaconda/bin/randomgenome.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 randomreads.sh -> ../../anaconda/bin/randomreads.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 rapmap -> ../../anaconda/bin/rapmap
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 razers3 -> ../../anaconda/bin/razers3
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 readlength.sh -> ../../anaconda/bin/readlength.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 readqc.sh -> ../../anaconda/bin/readqc.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 reducesilva.sh -> ../../anaconda/bin/reducesilva.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 reference2targets.py -> ../../anaconda/bin/reference2targets.py
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 reformat.sh -> ../../anaconda/bin/reformat.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 removebadbarcodes.sh -> ../../anaconda/bin/removebadbarcodes.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 15:55 removecatdogmousehuman.sh -> ../../anaconda/bin/removecatdogmousehuman.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 removeDup -> ../../anaconda/bin/removeDup
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 removehuman2.sh -> ../../anaconda/bin/removehuman2.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 removehuman.sh -> ../../anaconda/bin/removehuman.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 removemicrobes.sh -> ../../anaconda/bin/removemicrobes.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 removesmartbell.sh -> ../../anaconda/bin/removesmartbell.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 renameimg.sh -> ../../anaconda/bin/renameimg.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 rename.sh -> ../../anaconda/bin/rename.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 repair -> ../../anaconda/bin/repair
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 repair.sh -> ../../anaconda/bin/repair.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 replaceheaders.sh -> ../../anaconda/bin/replaceheaders.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 representative.sh -> ../../anaconda/bin/representative.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 reset -> ../../anaconda/bin/reset
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 RNA2Dfold -> ../../anaconda/bin/RNA2Dfold
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 RNAaliduplex -> ../../anaconda/bin/RNAaliduplex
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 RNAalifold -> ../../anaconda/bin/RNAalifold
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 RNAcofold -> ../../anaconda/bin/RNAcofold
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 RNAdistance -> ../../anaconda/bin/RNAdistance
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 RNAduplex -> ../../anaconda/bin/RNAduplex
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 RNAeval -> ../../anaconda/bin/RNAeval
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 RNAfold -> ../../anaconda/bin/RNAfold
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 RNAforester -> ../../anaconda/bin/RNAforester
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 RNAheat -> ../../anaconda/bin/RNAheat
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 RNAinverse -> ../../anaconda/bin/RNAinverse
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 RNALalifold -> ../../anaconda/bin/RNALalifold
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 RNALfold -> ../../anaconda/bin/RNALfold
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 RNAlocmin -> ../../anaconda/bin/RNAlocmin
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 RNApaln -> ../../anaconda/bin/RNApaln
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 RNAparconv -> ../../anaconda/bin/RNAparconv
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 RNApdist -> ../../anaconda/bin/RNApdist
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 RNAPKplex -> ../../anaconda/bin/RNAPKplex
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 RNAplex -> ../../anaconda/bin/RNAplex
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 RNAplfold -> ../../anaconda/bin/RNAplfold
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 RNAplot -> ../../anaconda/bin/RNAplot
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 RNApvmin -> ../../anaconda/bin/RNApvmin
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 RNAsnoop -> ../../anaconda/bin/RNAsnoop
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 rnaspades.py -> ../../anaconda/bin/rnaspades.py
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 RNAsubopt -> ../../anaconda/bin/RNAsubopt
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 RNAup -> ../../anaconda/bin/RNAup
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 16:06 roc -> ../../anaconda/envs/python2/bin/roc
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 rqcfilter2.sh -> ../../anaconda/bin/rqcfilter2.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 rqcfilter.sh -> ../../anaconda/bin/rqcfilter.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 rrbsreference -> ../../anaconda/bin/rrbsreference
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 Rscript -> ../../anaconda/bin/Rscript
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 rtg -> ../../anaconda/bin/rtg
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 run-bwamem -> ../../anaconda/bin/run-bwamem
lrwxrwxrwx 1 amizeranschi amizeranschi 45 Mar  3 16:06 run_metasv.py -> ../../anaconda/envs/python2/bin/run_metasv.py
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 RunRapMap.sh -> ../../anaconda/bin/RunRapMap.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 run-roh.pl -> ../../anaconda/bin/run-roh.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 67 Mar  3 16:06 runStrelkaGermlineWorkflowDemo.bash -> ../../anaconda/envs/python2/bin/runStrelkaGermlineWorkflowDemo.bash
lrwxrwxrwx 1 amizeranschi amizeranschi 66 Mar  3 16:06 runStrelkaSomaticWorkflowDemo.bash -> ../../anaconda/envs/python2/bin/runStrelkaSomaticWorkflowDemo.bash
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 16:06 RunTHetA.py -> ../../anaconda/envs/python2/bin/RunTHetA.py
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 sailfish -> ../../anaconda/bin/sailfish
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 salmon -> ../../anaconda/bin/salmon
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 sam2pindel -> ../../anaconda/bin/sam2pindel
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 sam2vcf.pl -> ../../anaconda/bin/sam2vcf.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 sambamba -> ../../anaconda/bin/sambamba
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 samblaster -> ../../anaconda/bin/samblaster
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 16:06 sam_juncs -> ../../anaconda/envs/python2/bin/sam_juncs
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 samtools -> ../../anaconda/bin/samtools
lrwxrwxrwx 1 amizeranschi amizeranschi 47 Mar  3 16:06 samtools_0.1.18 -> ../../anaconda/envs/python2/bin/samtools_0.1.18
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 samtools.pl -> ../../anaconda/bin/samtools.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 samtoroc.sh -> ../../anaconda/bin/samtoroc.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 scalpel-discovery -> ../../anaconda/bin/scalpel-discovery
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 scalpel-export -> ../../anaconda/bin/scalpel-export
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 16:06 scmp -> ../../anaconda/envs/python2/bin/scmp
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 scripts -> ../../anaconda/bin/scripts
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 seal.sh -> ../../anaconda/bin/seal.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 segmentFst -> ../../anaconda/bin/segmentFst
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 segmentIhs -> ../../anaconda/bin/segmentIhs
lrwxrwxrwx 1 amizeranschi amizeranschi 45 Mar  3 16:06 segment_juncs -> ../../anaconda/envs/python2/bin/segment_juncs
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 sem -> ../../anaconda/bin/sem
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 sendsketch.sh -> ../../anaconda/bin/sendsketch.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 16:06 sentieon -> ../../anaconda/envs/python2/bin/sentieon
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 16:06 sentieon-bwa -> ../../anaconda/envs/python2/bin/sentieon-bwa
lrwxrwxrwx 1 amizeranschi amizeranschi 48 Mar  3 16:06 sentieon-licsrvr -> ../../anaconda/envs/python2/bin/sentieon-licsrvr
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 seq2cov.pl -> ../../anaconda/bin/seq2cov.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 15:55 seq_cache_populate.pl -> ../../anaconda/bin/seq_cache_populate.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 seqtk -> ../../anaconda/bin/seqtk
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 sequenceDiversity -> ../../anaconda/bin/sequenceDiversity
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 shiftBed -> ../../anaconda/bin/shiftBed
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 shred.sh -> ../../anaconda/bin/shred.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 shrinkaccession.sh -> ../../anaconda/bin/shrinkaccession.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 shuffle2.sh -> ../../anaconda/bin/shuffle2.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 shuffleBed -> ../../anaconda/bin/shuffleBed
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 shuffle.sh -> ../../anaconda/bin/shuffle.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 sickle -> ../../anaconda/bin/sickle
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 15:55 simple_sv_annotation.py -> ../../anaconda/bin/simple_sv_annotation.py
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 sketchblacklist.sh -> ../../anaconda/bin/sketchblacklist.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 sketch.sh -> ../../anaconda/bin/sketch.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 skg_convert.py -> ../../anaconda/bin/skg_convert.py
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 slopBed -> ../../anaconda/bin/slopBed
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 16:06 smCounter2 -> ../../anaconda/envs/python2/bin/smCounter2
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 smoother -> ../../anaconda/bin/smoother
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 16:06 smoove -> ../../anaconda/envs/python2/bin/smoove
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 snap-aligner -> ../../anaconda/bin/snap-aligner
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 snpEff -> ../../anaconda/bin/snpEff
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 soap2sam.pl -> ../../anaconda/bin/soap2sam.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 16:06 som.py -> ../../anaconda/envs/python2/bin/som.py
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 sortBed -> ../../anaconda/bin/sortBed
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 sortbyname.sh -> ../../anaconda/bin/sortbyname.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 48 Mar  3 16:06 sortedcontainers -> ../../anaconda/envs/python2/bin/sortedcontainers
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 spades-bwa -> ../../anaconda/bin/spades-bwa
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 spades-core -> ../../anaconda/bin/spades-core
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 15:55 spades-corrector-core -> ../../anaconda/bin/spades-corrector-core
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 spades-gbuilder -> ../../anaconda/bin/spades-gbuilder
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 spades-gmapper -> ../../anaconda/bin/spades-gmapper
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 spades-hammer -> ../../anaconda/bin/spades-hammer
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 spades_init.py -> ../../anaconda/bin/spades_init.py
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 spades-ionhammer -> ../../anaconda/bin/spades-ionhammer
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 spades-kmercount -> ../../anaconda/bin/spades-kmercount
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 spades.py -> ../../anaconda/bin/spades.py
lrwxrwxrwx 1 amizeranschi amizeranschi 46 Mar  3 15:55 spades-truseq-scfcorrection -> ../../anaconda/bin/spades-truseq-scfcorrection
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 splitbytaxa.sh -> ../../anaconda/bin/splitbytaxa.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 splitnextera.sh -> ../../anaconda/bin/splitnextera.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 splitsam4way.sh -> ../../anaconda/bin/splitsam4way.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 splitsam6way.sh -> ../../anaconda/bin/splitsam6way.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 splitsam.sh -> ../../anaconda/bin/splitsam.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 sponge -> ../../anaconda/bin/sponge
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 sql -> ../../anaconda/bin/sql
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 16:06 sra_to_solid -> ../../anaconda/envs/python2/bin/sra_to_solid
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 STAR -> ../../anaconda/bin/STAR
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 STARlong -> ../../anaconda/bin/STARlong
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 stats.sh -> ../../anaconda/bin/stats.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 statswrapper.sh -> ../../anaconda/bin/statswrapper.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 streamsam.sh -> ../../anaconda/bin/streamsam.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 stringtie -> ../../anaconda/bin/stringtie
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 subindel -> ../../anaconda/bin/subindel
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 subjunc -> ../../anaconda/bin/subjunc
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 sublong -> ../../anaconda/bin/sublong
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 subread-align -> ../../anaconda/bin/subread-align
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 subread-buildindex -> ../../anaconda/bin/subread-buildindex
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 subread-fullscan -> ../../anaconda/bin/subread-fullscan
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 subtractBed -> ../../anaconda/bin/subtractBed
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 summarizecontam.sh -> ../../anaconda/bin/summarizecontam.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 15:55 summarizecrossblock.sh -> ../../anaconda/bin/summarizecrossblock.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 summarizemerge.sh -> ../../anaconda/bin/summarizemerge.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 summarizequast.sh -> ../../anaconda/bin/summarizequast.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 15:55 summarizescafstats.sh -> ../../anaconda/bin/summarizescafstats.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 summarizeseal.sh -> ../../anaconda/bin/summarizeseal.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 summarizesketch.sh -> ../../anaconda/bin/summarizesketch.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 SURVIVOR -> ../../anaconda/bin/SURVIVOR
lrwxrwxrwx 1 amizeranschi amizeranschi 48 Mar  3 16:06 sv_classifier.py -> ../../anaconda/envs/python2/bin/sv_classifier.py
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 16:06 svtools -> ../../anaconda/envs/python2/bin/svtools
lrwxrwxrwx 1 amizeranschi amizeranschi 48 Mar  3 16:06 svtool_to_vcf.py -> ../../anaconda/envs/python2/bin/svtool_to_vcf.py
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 16:06 svtyper -> ../../anaconda/envs/python2/bin/svtyper
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 16:06 svtyper-sso -> ../../anaconda/envs/python2/bin/svtyper-sso
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 synthmda.sh -> ../../anaconda/bin/synthmda.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 tabix -> ../../anaconda/bin/tabix
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 tabs -> ../../anaconda/bin/tabs
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 tadpipe.sh -> ../../anaconda/bin/tadpipe.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 tadpole.sh -> ../../anaconda/bin/tadpole.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 tadwrapper.sh -> ../../anaconda/bin/tadwrapper.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 tagBam -> ../../anaconda/bin/tagBam
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 taxonomy.sh -> ../../anaconda/bin/taxonomy.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 taxserver.sh -> ../../anaconda/bin/taxserver.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 taxsize.sh -> ../../anaconda/bin/taxsize.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 taxtree.sh -> ../../anaconda/bin/taxtree.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 TdrMappingScripts.pl -> ../../anaconda/bin/TdrMappingScripts.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 testfilesystem.sh -> ../../anaconda/bin/testfilesystem.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 testformat2.sh -> ../../anaconda/bin/testformat2.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 testformat.sh -> ../../anaconda/bin/testformat.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 47 Mar  3 16:06 test_haplotypes -> ../../anaconda/envs/python2/bin/test_haplotypes
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 testsomatic.R -> ../../anaconda/bin/testsomatic.R
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 teststrandbias.R -> ../../anaconda/bin/teststrandbias.R
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 tetramerfreq.sh -> ../../anaconda/bin/tetramerfreq.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 textfile.sh -> ../../anaconda/bin/textfile.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 tic -> ../../anaconda/bin/tic
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 toe -> ../../anaconda/bin/toe
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 16:06 tophat -> ../../anaconda/envs/python2/bin/tophat
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 16:06 tophat2 -> ../../anaconda/envs/python2/bin/tophat2
lrwxrwxrwx 1 amizeranschi amizeranschi 50 Mar  3 16:06 tophat-fusion-post -> ../../anaconda/envs/python2/bin/tophat-fusion-post
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 tophat-recondition -> ../../anaconda/bin/tophat-recondition
lrwxrwxrwx 1 amizeranschi amizeranschi 46 Mar  3 16:06 tophat_reports -> ../../anaconda/envs/python2/bin/tophat_reports
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 tput -> ../../anaconda/bin/tput
lrwxrwxrwx 1 amizeranschi amizeranschi 38 Mar  3 15:55 translate6frames.sh -> ../../anaconda/bin/translate6frames.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 trmap -> ../../anaconda/bin/trmap
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 truspades.py -> ../../anaconda/bin/truspades.py
lrwxrwxrwx 1 amizeranschi amizeranschi 21 Mar  3 15:55 ts -> ../../anaconda/bin/ts
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 tset -> ../../anaconda/bin/tset
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 txUnique -> ../../anaconda/bin/txUnique
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 umis -> ../../anaconda/bin/umis
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 unicode2ascii.sh -> ../../anaconda/bin/unicode2ascii.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 unionBedGraphs -> ../../anaconda/bin/unionBedGraphs
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 unlzma -> ../../anaconda/bin/unlzma
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 unxz -> ../../anaconda/bin/unxz
lrwxrwxrwx 1 amizeranschi amizeranschi 46 Mar  3 16:06 update_info.py -> ../../anaconda/envs/python2/bin/update_info.py
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 16:06 validatevcf -> ../../anaconda/envs/python2/bin/validatevcf
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 var2vcf_paired.pl -> ../../anaconda/bin/var2vcf_paired.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 var2vcf_valid.pl -> ../../anaconda/bin/var2vcf_valid.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 vardict -> ../../anaconda/bin/vardict
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 vardict2mut.pl -> ../../anaconda/bin/vardict2mut.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 vardict-java -> ../../anaconda/bin/vardict-java
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vardict.pl -> ../../anaconda/bin/vardict.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 16:06 varfilter.py -> ../../anaconda/envs/python2/bin/varfilter.py
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 variant -> ../../anaconda/bin/variant
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 variant_recoder -> ../../anaconda/bin/variant_recoder
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 varscan -> ../../anaconda/bin/varscan
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 16:06 vawk -> ../../anaconda/envs/python2/bin/vawk
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcf2bed.py -> ../../anaconda/bin/vcf2bed.py
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 vcf2dag -> ../../anaconda/bin/vcf2dag
lrwxrwxrwx 1 amizeranschi amizeranschi 41 Mar  3 16:06 vcf2db.py -> ../../anaconda/envs/python2/bin/vcf2db.py
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 vcf2fasta -> ../../anaconda/bin/vcf2fasta
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcf2gff.sh -> ../../anaconda/bin/vcf2gff.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 vcf2sqlite.py -> ../../anaconda/bin/vcf2sqlite.py
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 vcf2tsv -> ../../anaconda/bin/vcf2tsv
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcfaddinfo -> ../../anaconda/bin/vcfaddinfo
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 vcfafpath -> ../../anaconda/bin/vcfafpath
lrwxrwxrwx 1 amizeranschi amizeranschi 50 Mar  3 16:06 vcf_allele_freq.py -> ../../anaconda/envs/python2/bin/vcf_allele_freq.py
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 vcfallelicprimitives -> ../../anaconda/bin/vcfallelicprimitives
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfaltcount -> ../../anaconda/bin/vcfaltcount
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 vcfanno -> ../../anaconda/bin/vcfanno
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfannotate -> ../../anaconda/bin/vcfannotate
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 vcfannotategenotypes -> ../../anaconda/bin/vcfannotategenotypes
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 vcfbiallelic -> ../../anaconda/bin/vcfbiallelic
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 vcfbreakmulti -> ../../anaconda/bin/vcfbreakmulti
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 vcfcat -> ../../anaconda/bin/vcfcat
lrwxrwxrwx 1 amizeranschi amizeranschi 40 Mar  3 16:36 vcfcheck -> ../../anaconda/envs/python2/bin/vcfcheck
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfclassify -> ../../anaconda/bin/vcfclassify
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 vcfcleancomplex -> ../../anaconda/bin/vcfcleancomplex
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcfclearid -> ../../anaconda/bin/vcfclearid
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 vcfclearinfo -> ../../anaconda/bin/vcfclearinfo
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcfcombine -> ../../anaconda/bin/vcfcombine
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 vcfcommonsamples -> ../../anaconda/bin/vcfcommonsamples
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcfcomplex -> ../../anaconda/bin/vcfcomplex
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 vcfcountalleles -> ../../anaconda/bin/vcfcountalleles
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 vcfcreatemulti -> ../../anaconda/bin/vcfcreatemulti
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfdistance -> ../../anaconda/bin/vcfdistance
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 vcfecho -> ../../anaconda/bin/vcfecho
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcfentropy -> ../../anaconda/bin/vcfentropy
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 vcfevenregions -> ../../anaconda/bin/vcfevenregions
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 vcffilter -> ../../anaconda/bin/vcffilter
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 vcffirstheader -> ../../anaconda/bin/vcffirstheader
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 vcffixup -> ../../anaconda/bin/vcffixup
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcfflatten -> ../../anaconda/bin/vcfflatten
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 vcfgeno2alleles -> ../../anaconda/bin/vcfgeno2alleles
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 vcfgeno2haplo -> ../../anaconda/bin/vcfgeno2haplo
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 vcfgenosamplenames -> ../../anaconda/bin/vcfgenosamplenames
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 vcfgenosummarize -> ../../anaconda/bin/vcfgenosummarize
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 vcfgenotypecompare -> ../../anaconda/bin/vcfgenotypecompare
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 vcfgenotypes -> ../../anaconda/bin/vcfgenotypes
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcfglbound -> ../../anaconda/bin/vcfglbound
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 vcfglxgt -> ../../anaconda/bin/vcfglxgt
lrwxrwxrwx 1 amizeranschi amizeranschi 54 Mar  3 16:06 vcf_group_multiline.py -> ../../anaconda/envs/python2/bin/vcf_group_multiline.py
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 vcfgtcompare.sh -> ../../anaconda/bin/vcfgtcompare.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 16:06 vcfhdr2json -> ../../anaconda/envs/python2/bin/vcfhdr2json
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfhetcount -> ../../anaconda/bin/vcfhetcount
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 vcfhethomratio -> ../../anaconda/bin/vcfhethomratio
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 vcfindelproximity -> ../../anaconda/bin/vcfindelproximity
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 vcfindels -> ../../anaconda/bin/vcfindels
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 vcfindex -> ../../anaconda/bin/vcfindex
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 vcfinfo2qual -> ../../anaconda/bin/vcfinfo2qual
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 vcfinfosummarize -> ../../anaconda/bin/vcfinfosummarize
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 vcfintersect -> ../../anaconda/bin/vcfintersect
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 vcfjoincalls -> ../../anaconda/bin/vcfjoincalls
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfkeepgeno -> ../../anaconda/bin/vcfkeepgeno
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfkeepinfo -> ../../anaconda/bin/vcfkeepinfo
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 vcfkeepsamples -> ../../anaconda/bin/vcfkeepsamples
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 vcfld -> ../../anaconda/bin/vcfld
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 vcfleftalign -> ../../anaconda/bin/vcfleftalign
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 vcflength -> ../../anaconda/bin/vcflength
lrwxrwxrwx 1 amizeranschi amizeranschi 52 Mar  3 16:06 vcf_modify_header.py -> ../../anaconda/envs/python2/bin/vcf_modify_header.py
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 vcfmultiallelic -> ../../anaconda/bin/vcfmultiallelic
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfmultiway -> ../../anaconda/bin/vcfmultiway
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 vcfmultiwayscripts -> ../../anaconda/bin/vcfmultiwayscripts
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 vcfnobiallelicsnps -> ../../anaconda/bin/vcfnobiallelicsnps
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfnoindels -> ../../anaconda/bin/vcfnoindels
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 vcfnormalizesvs -> ../../anaconda/bin/vcfnormalizesvs
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 vcfnosnps -> ../../anaconda/bin/vcfnosnps
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfnull2ref -> ../../anaconda/bin/vcfnull2ref
lrwxrwxrwx 1 amizeranschi amizeranschi 37 Mar  3 15:55 vcfnulldotslashdot -> ../../anaconda/bin/vcfnulldotslashdot
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 vcfnumalt -> ../../anaconda/bin/vcfnumalt
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcfoverlay -> ../../anaconda/bin/vcfoverlay
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 vcfparsealts -> ../../anaconda/bin/vcfparsealts
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 16:06 vcf_paste.py -> ../../anaconda/envs/python2/bin/vcf_paste.py
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 15:55 vcfplotaltdiscrepancy.r -> ../../anaconda/bin/vcfplotaltdiscrepancy.r
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 15:55 vcfplotaltdiscrepancy.sh -> ../../anaconda/bin/vcfplotaltdiscrepancy.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 15:55 vcfplotsitediscrepancy.r -> ../../anaconda/bin/vcfplotsitediscrepancy.r
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 vcfplottstv.sh -> ../../anaconda/bin/vcfplottstv.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcfprimers -> ../../anaconda/bin/vcfprimers
lrwxrwxrwx 1 amizeranschi amizeranschi 43 Mar  3 15:55 vcfprintaltdiscrepancy.r -> ../../anaconda/bin/vcfprintaltdiscrepancy.r
lrwxrwxrwx 1 amizeranschi amizeranschi 44 Mar  3 15:55 vcfprintaltdiscrepancy.sh -> ../../anaconda/bin/vcfprintaltdiscrepancy.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 vcfqual2info -> ../../anaconda/bin/vcfqual2info
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 vcfqualfilter -> ../../anaconda/bin/vcfqualfilter
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 vcfrandom -> ../../anaconda/bin/vcfrandom
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 vcfrandomsample -> ../../anaconda/bin/vcfrandomsample
lrwxrwxrwx 1 amizeranschi amizeranschi 34 Mar  3 15:55 vcfregionreduce -> ../../anaconda/bin/vcfregionreduce
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 15:55 vcfregionreduce_and_cut -> ../../anaconda/bin/vcfregionreduce_and_cut
lrwxrwxrwx 1 amizeranschi amizeranschi 39 Mar  3 15:55 vcfregionreduce_pipe -> ../../anaconda/bin/vcfregionreduce_pipe
lrwxrwxrwx 1 amizeranschi amizeranschi 47 Mar  3 15:55 vcfregionreduce_uncompressed -> ../../anaconda/bin/vcfregionreduce_uncompressed
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 vcfremap -> ../../anaconda/bin/vcfremap
lrwxrwxrwx 1 amizeranschi amizeranschi 45 Mar  3 15:55 vcfremoveaberrantgenotypes -> ../../anaconda/bin/vcfremoveaberrantgenotypes
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 vcfremovenonATGC -> ../../anaconda/bin/vcfremovenonATGC
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 vcfremovesamples -> ../../anaconda/bin/vcfremovesamples
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 vcfroc -> ../../anaconda/bin/vcfroc
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 vcfsample2info -> ../../anaconda/bin/vcfsample2info
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 vcfsamplediff -> ../../anaconda/bin/vcfsamplediff
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 vcfsamplenames -> ../../anaconda/bin/vcfsamplenames
lrwxrwxrwx 1 amizeranschi amizeranschi 35 Mar  3 15:55 vcfsitesummarize -> ../../anaconda/bin/vcfsitesummarize
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 vcfsnps -> ../../anaconda/bin/vcfsnps
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 vcfsort -> ../../anaconda/bin/vcfsort
lrwxrwxrwx 1 amizeranschi amizeranschi 27 Mar  3 15:55 vcfstats -> ../../anaconda/bin/vcfstats
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 vcfstreamsort -> ../../anaconda/bin/vcfstreamsort
lrwxrwxrwx 1 amizeranschi amizeranschi 42 Mar  3 15:55 vcf_strip_extra_headers -> ../../anaconda/bin/vcf_strip_extra_headers
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 vcfuniq -> ../../anaconda/bin/vcfuniq
lrwxrwxrwx 1 amizeranschi amizeranschi 33 Mar  3 15:55 vcfuniqalleles -> ../../anaconda/bin/vcfuniqalleles
lrwxrwxrwx 1 amizeranschi amizeranschi 29 Mar  3 15:55 vcfunphase -> ../../anaconda/bin/vcfunphase
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfutils.pl -> ../../anaconda/bin/vcfutils.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vcfvarstats -> ../../anaconda/bin/vcfvarstats
lrwxrwxrwx 1 amizeranschi amizeranschi 22 Mar  3 15:55 vep -> ../../anaconda/bin/vep
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 15:55 vep_convert_cache -> ../../anaconda/bin/vep_convert_cache
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 vep_install -> ../../anaconda/bin/vep_install
lrwxrwxrwx 1 amizeranschi amizeranschi 31 Mar  3 15:55 verifybamid2 -> ../../anaconda/bin/verifybamid2
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 vidir -> ../../anaconda/bin/vidir
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 vipe -> ../../anaconda/bin/vipe
lrwxrwxrwx 1 amizeranschi amizeranschi 21 Mar  3 15:55 vt -> ../../anaconda/bin/vt
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 wcFst -> ../../anaconda/bin/wcFst
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 webcheck.sh -> ../../anaconda/bin/webcheck.sh
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 wgsim -> ../../anaconda/bin/wgsim
lrwxrwxrwx 1 amizeranschi amizeranschi 32 Mar  3 15:55 wgsim_eval.pl -> ../../anaconda/bin/wgsim_eval.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 wham -> ../../anaconda/bin/wham
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 whamg -> ../../anaconda/bin/whamg
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 wigToBigWig -> ../../anaconda/bin/wigToBigWig
lrwxrwxrwx 1 amizeranschi amizeranschi 28 Mar  3 15:55 windowBed -> ../../anaconda/bin/windowBed
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 windowMaker -> ../../anaconda/bin/windowMaker
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 xa2multi.pl -> ../../anaconda/bin/xa2multi.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 36 Mar  3 16:06 xcmp -> ../../anaconda/envs/python2/bin/xcmp
lrwxrwxrwx 1 amizeranschi amizeranschi 21 Mar  3 15:55 xz -> ../../anaconda/bin/xz
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 xzcat -> ../../anaconda/bin/xzcat
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 xzcmp -> ../../anaconda/bin/xzcmp
lrwxrwxrwx 1 amizeranschi amizeranschi 24 Mar  3 15:55 xzdec -> ../../anaconda/bin/xzdec
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 xzdiff -> ../../anaconda/bin/xzdiff
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 xzegrep -> ../../anaconda/bin/xzegrep
lrwxrwxrwx 1 amizeranschi amizeranschi 26 Mar  3 15:55 xzfgrep -> ../../anaconda/bin/xzfgrep
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 xzgrep -> ../../anaconda/bin/xzgrep
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 xzless -> ../../anaconda/bin/xzless
lrwxrwxrwx 1 amizeranschi amizeranschi 25 Mar  3 15:55 xzmore -> ../../anaconda/bin/xzmore
lrwxrwxrwx 1 amizeranschi amizeranschi 30 Mar  3 15:55 zoom2sam.pl -> ../../anaconda/bin/zoom2sam.pl
lrwxrwxrwx 1 amizeranschi amizeranschi 23 Mar  3 15:55 zrun -> ../../anaconda/bin/zrun
chapmanb commented 5 years ago

Thanks for the question. You're right that tools from bcbiovm don't get linked into the main bin directory, except for bcbio_vm.py itself. This is intentional, specifically to avoid overlinking files from the base bcbio installation where they overlap.

The calls to bcbio inject the right path in when running to avoid needing to symlink them:

https://github.com/bcbio/bcbio-nextgen/blob/9a7851a07c5a065570fdb93285d9b4d740d5b80a/bcbio/cwl/tool.py#L42

and to keep it excluded. However, this is at the end of the path so if you have other tools installed that mask them it will use those first.

If it would be useful to symlink some high level tools, like Cromwell and cwltools, into the bin directory we could do.

Thank again for the discussion.

amizeranschi commented 5 years ago

Thanks for the reply and the clarification. It might still be useful to symlink tools like cromwell, cwltool and toil (if it'll make it back into the bcbio tool-chain) inside the bcbio_nextgen/tools/bin directory. This could help to prevent some situations such as the one mentioned here: https://github.com/bcbio/bcbio-nextgen/issues/2697#issuecomment-468956231.