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ndaniel / fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data
GNU General Public License v3.0
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Wrong version of BOWTIE found #36

Closed komalsrathi closed 7 years ago

komalsrathi commented 7 years ago

Hi,

So I install fusioncatcher and the data separately like this:

wget http://sf.net/projects/fusioncatcher/files/bootstrap.py -O $bin/bootstrap.py
python2.6 $bin/bootstrap.py --install-all --yes -t
bash $bin/fusioncatcher/fusioncatcher_v0.99.7b/bin/download.sh

The installation did not throw any errors but when I went to test the installation:

/mnt/isilon/cbmi/variome/bin/fusioncatcher/test/test.sh

It gave me test not ok:

ERROR: Wrong version of BOWTIE found (/mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/bowtie/bowtie)! It should be 'bowtie-align version 1.2'. One may specify the path to the correct version in 'fusioncatcher/etc/configuration.cfg'.

sort: open failed: test_fusioncatcher/summary_candidate_fusions.txt: No such file or directory

The one that is in the etc/configuration.cfg file is:

$ head configuration.cfg 
[paths]
python = /usr/bin
data = /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/current
scripts = /mnt/isilon/cbmi/variome/bin/fusioncatcher/bin
bowtie = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/bowtie
bowtie2 = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/bowtie2

Here are all the bowtie installations:

$ ls /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/
1.0-r82b         biopython-1.68           bowtie-1.2-linux-x86_64.zip     liftover                  setuptools                       sratoolkit.2.6.2-centos_linux64.tar.gz
1.0-r82b.tar.gz  biopython-1.68.tar.gz    bowtie2                         openpyxl                  setuptools-20.9.0                star
2.5.2b           blat                     bowtie2-2.2.9-linux-x86_64      openpyxl-2.4.0-a1         setuptools-20.9.0.tar.gz         xlrd
2.5.2b.tar.gz    bowtie                   bowtie2-2.2.9-linux-x86_64.zip  openpyxl-2.4.0-a1.tar.gz  sratoolkit                       xlrd-0.9.4
biopython        bowtie-1.2-linux-x86_64  fatotwobit                      seqtk                     sratoolkit.2.6.2-centos_linux64  xlrd-0.9.4.tar.gz

$ ls /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/bowtie-1.2-linux-x86_64/
AUTHORS                 bowtie-align-s          bowtie-build-l-debug    bowtie-inspect-l        doc/                    MANUAL                  scripts/
bowtie                  bowtie-align-s-debug    bowtie-build-s          bowtie-inspect-l-debug  genomes/                MANUAL.markdown         SeqAn-1.1/
bowtie-align-l          bowtie-build            bowtie-build-s-debug    bowtie-inspect-s        indexes/                NEWS                    TUTORIAL
bowtie-align-l-debug    bowtie-build-l          bowtie-inspect          bowtie-inspect-s-debug  LICENSE                 reads/                  VERSION

However, none of the bowtie installations were ok because when I try to print out the version, it throws me this error:

$ /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/bowtie/bowtie -version
bowtie-align: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory

$ /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/bowtie-1.2-linux-x86_64/bowtie --version
bowtie-align: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory

Can you suggest a possible solution for this?

ndaniel commented 7 years ago

Hi!

The configuration.cfg file looks good!

If you run manually this in a terminal:

/mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/bowtie/bowtie --version

what does it show?

This might be similar to this https://github.com/ndaniel/fusioncatcher/issues/34 which was solved by running sudo apt-get install libtbb2.

komalsrathi commented 7 years ago

It is in my question - the bowtie installation wasn't correct:

$ /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/bowtie/bowtie -version
bowtie-align: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory

I don't know why it failed.

komalsrathi commented 7 years ago

I don't have sudo rights but I can ask the sys admin to do it. Thanks!

komalsrathi commented 7 years ago

I got that installed but now I am getting another library issue - libtbbmalloc_proxy.so.2

ndaniel commented 7 years ago

Hi,

that needs

sudo apt-get install libtbb-dev

See: https://github.com/ndaniel/fusioncatcher/issues/31

Cheers, Daniel

On Mar 15, 2017 20:08, "Komal Rathi" notifications@github.com wrote:

I got that installed but now I am getting another library issue - libtbbmalloc_proxy.so.2

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ndaniel/fusioncatcher/issues/36#issuecomment-286830690, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJ2i2fX9mIbF6kX5knA1fjUc9f36vTVks5rmCkdgaJpZM4MeAU7 .

ndaniel commented 7 years ago

From https://sourceforge.net/projects/fusioncatcher/files/README.md/download one has

Download / Install / Update FusionCatcher

Use this one-line command:

wget http://sf.net/projects/fusioncatcher/files/bootstrap.py -O bootstrap.py && python bootstrap.py -t --download
If one wants to have all the questions asked by boostrap.py answered automatically with yes then add -y to command above. For more see:

bootstrap.py --help
In Ubuntu running this command before installing FusionCatcher would make the installation smoother:

sudo apt-get install wget gawk gcc g++ make cmake curl unzip zip tar gzip pigz build-essential libncurses5-dev zlib1g-dev libtbb-dev libtbb2 python python-dev python-numpy python-biopython python-xlrd python-openpyxl
komalsrathi commented 7 years ago

Ok I got that working but after fixing that I got another error:

$ ./bowtie --version
bowtie-align: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by bowtie-align)

I am working with the systems engineer here to install these requirements but just want to keep you updated - if at all its helpful.

komalsrathi commented 7 years ago

Can I change the .cfg file to point to any currently installed bowtie version?

ndaniel commented 7 years ago

Hi,

you may change the .cfg file to point to another installed bowtie installation *if only and only* that bowtie is version 1.2.0.

On the other hand does this solve the issue "/lib64/libc.so.6: not found":

sudo apt-get install libc6-dev
sudo ln -s /lib64/x86_64-linux-gnu/libc.so.6 /lib64/libc.so.6

Are you using an Ubuntu/Debin computer for installing FusionCacher?

FusionCatcher basically just copies the Bowtie's executable, which is dynamically linked, during the installation. I looked to issues regarding Bowtie, here https://github.com/BenLangmead/bowtie/issues , but I have not seen any close to bowtie-align: /lib64/libc.so.6: versionGLIBC_2.14' not found (required by bowtie-align)`.

Another workaround might be to use the legacy version of Bowtie 1.2 (that is https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.0/bowtie-1.2-linux-legacy-x86_64.zip) instead of the default one (that is https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.0/bowtie-1.2-linux-x86_64.zip ). I have not tried this so I do not know how well this would work.

komalsrathi commented 7 years ago

I was successfully able to install it - the test is still running (STAR is taking a long time) but I am positive that it was installed ok after loading all the libraries. Thanks!!

ndaniel commented 7 years ago

The test should run in approx. 5 to 20 minutes. If it lasts more than that then it might be a problem.

komalsrathi commented 7 years ago

I am not sure then - because the first time my test took so long, I hit tried to kill it then it started a second attempt which ran for like 7 hours and then I had to kill it:

These are the final lines of the installation using python2.6 bootstrap.py --install-all --yes -t:

FusionCatcher is installed here:
  /mnt/isilon/cbmi/variome/bin/fusioncatcher
FusionCatcher's scripts are here:
  /mnt/isilon/cbmi/variome/bin/fusioncatcher/bin
FusionCatcher's dependencies and tools are installed here:
  /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools
FusionCatcher's organism data is here:
  /mnt/isilon/cbmi/variome/bin/fusioncatcher/data
Run FusionCatcher as following:
  /mnt/isilon/cbmi/variome/bin/fusioncatcher/bin/fusioncatcher
In order to download and build the files for FusionCatcher run the following:
  /mnt/isilon/cbmi/variome/bin/fusioncatcher/bin/fusioncatcher-build

=== Installed successfully! ===

*****************************************************************
*  DON'T FORGET to download (or build) the organism's data needed by FusionCatcher to run!
*****************************************************************

Several options to get the data needed by FusionCatcher are shown below (please try them in this order)!

---------------------------------------------------------------------------
*  OPTION 1: Download the data needed by FusionCatcher from SOURCEFORGE!
             THIS IS HIGHLY RECOMMENDED
---------------------------------------------------------------------------
In order to download the latest human data files needed by FusionCatcher, please run these (it will take several hours):

rm -rf /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/current
rm -f /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86.tar.gz.*
rm -rf /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86
rm -f /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/checksums.md5
mkdir -p /mnt/isilon/cbmi/variome/bin/fusioncatcher/data
ln -s /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86 /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/current
wget --no-check-certificate http://sourceforge.net/projects/fusioncatcher/files/data/ensembl_v86.tar.gz.aa -O /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86.tar.gz.aa
wget --no-check-certificate http://sourceforge.net/projects/fusioncatcher/files/data/ensembl_v86.tar.gz.ab -O /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86.tar.gz.ab
wget --no-check-certificate http://sourceforge.net/projects/fusioncatcher/files/data/ensembl_v86.tar.gz.ac -O /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86.tar.gz.ac
wget --no-check-certificate http://sourceforge.net/projects/fusioncatcher/files/data/ensembl_v86.tar.gz.ad -O /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86.tar.gz.ad
wget --no-check-certificate http://sourceforge.net/projects/fusioncatcher/files/data/checksums.md5 -O /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/checksums.md5
cd /mnt/isilon/cbmi/variome/bin/fusioncatcher/data
md5sum -c /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/checksums.md5
if [ "$?" -ne "0" ]; then
  echo -e "\n\n\n\033[33;7m   ERROR: The downloaded files from above have errors! MD5 checksums do not match! Please, download them again or re-run this script again!   \033[0m\n"
  exit 1
fi
cat /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86.tar.gz.* > /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86.tar.gz
rm -f /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86.tar.gz.*
if ! tar -xzf /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86.tar.gz -C /mnt/isilon/cbmi/variome/bin/fusioncatcher/data; then
    echo -e "\n\n\n\033[33;7m   ERROR: The downloaded files are corrupted!   \033[0m\n"
    exit 1
fi
rm -f /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/ensembl_v86.tar.gz
rm -f /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/checksums.md5

All these commands are saved in '/mnt/isilon/cbmi/variome/bin/fusioncatcher/bin/download.sh' file! You may execute '/mnt/isilon/cbmi/variome/bin/fusioncatcher/bin/download.sh' shell script or copy/paste all the previous commands and run them manually in the terminal!

---------------------------------------------------------------------------
*  OPTION 2: Build yourself the data needed by FusionCatcher!
             TRY THIS ONLY IF OPTION 1 and OPTION 2 DID NOT WORK!
---------------------------------------------------------------------------
In order to build yourself the latest human data files needed by FusionCatcher, please run these (it will take several hours):

rm  -rf  /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/current
rm  -rf  /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/v87
mkdir  -p  /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/v87
ln  -s  /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/v87  /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/current
/mnt/isilon/cbmi/variome/bin/fusioncatcher/bin/fusioncatcher-build  -g  homo_sapiens  -o /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/v87

All these commands are saved in '/mnt/isilon/cbmi/variome/bin/fusioncatcher/bin/build.sh' file! You may execute '/mnt/isilon/cbmi/variome/bin/fusioncatcher/bin/build.sh' shell script or copy/paste all the previous commands and run them manually in the terminal!

---------------------------------------------------------------------------

--------------> THE END! <---------------------------

*****************************************************************
*  DON'T FORGET to download (or build) the organism's data needed
   by FusionCatcher to run (see above for options)!

test directory structure:

|-- test
|   |-- final-list_candidate-fusion-genes.txt
|   |-- readme.txt
|   |-- reads_1.fq.gz
|   |-- reads_2.fq.gz
|   |-- summary_candidate_fusions.txt
|   `-- test.sh

I just run ./test.sh:

Mar 16 14:19:53 ..... started STAR run
Mar 16 14:19:53 ..... loading genome
Mar 16 14:20:01 ..... started 1st pass mapping
Mar 16 14:20:08 ..... finished 1st pass mapping
Mar 16 14:20:08 ..... inserting junctions into the genome indices
Mar 16 14:20:19 ..... started mapping
Mar 16 14:20:24 ..... finished successfully

^C

ERROR: Workflow execution failed at step 359 while executing:
----------------
   STAR \
   --twopass1readsN -1 \
   --twopassMode Basic \
   --genomeSAindexNbases 14 \
   --sjdbOverhang 100 \
   --alignIntronMax 972692 \
   --outFilterMatchNmin 16 \
   --outFilterMatchNminOverLread 0.2667 \
   --outFilterScoreMinOverLread 0.2667 \
   --alignSplicedMateMapLminOverLmate 0.2667 \
   --genomeDir /mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/test/test_fusioncatcher/gene-gene-star/ \
   --runThreadN 16 \
   --seedSearchStartLmax 16 \
   --alignSJoverhangMin 16 \
   --alignSJstitchMismatchNmax 5 -1 5 5 \
   --outSJfilterOverhangMin 10 10 10 10 \
   --outSJfilterCountUniqueMin 1 1 1 1 \
   --outSJfilterCountTotalMin 1 1 1 1 \
   --outSJfilterDistToOtherSJmin 0 0 0 0 \
   --outSJfilterIntronMaxVsReadN 972692 972692 972692 \
   --limitOutSAMoneReadBytes 100000000 \
   --scoreGapNoncan -4 \
   --scoreGapATAC -4 \
   --readFilesIn /mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/test/test_fusioncatcher/reads_gene-gene_no-str_fixed.fq \
   --outFileNamePrefix /mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/test/test_fusioncatcher/gene-gene-star-results/
----------------
  * Size '/mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/test/test_fusioncatcher/star_sdjboverhang.txt' = 3 bytes
  * Size '/mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/test/test_fusioncatcher/gene-gene_longest.txt' = 6 bytes
  * Size '/mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/test/test_fusioncatcher/gene-gene-star/' = 1665246217 bytes
  * Size '/mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/test/test_fusioncatcher/reads_gene-gene_no-str_fixed.fq' = 550618 bytes
  * Size '/mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/test/test_fusioncatcher/gene-gene-star-results/' = 1602013 bytes

Executing second time the same step/command in order to capture error messages (i.e. STDERR)...

-------------------------------------------
Mar 16 14:48:12 ..... started STAR run
Mar 16 14:48:12 ..... loading genome
Mar 16 14:48:30 ..... started 1st pass mapping
Mar 16 14:48:35 ..... finished 1st pass mapping
Mar 16 14:48:35 ..... inserting junctions into the genome indices
Mar 16 14:48:46 ..... started mapping
Mar 16 14:48:50 ..... finished successfully

^C################################################################################
################################################################################
TOTAL RUNNING TIME: 0 day(s), 7 hour(s), 48 minute(s), and 15 second(s) 
################################################################################
################################################################################
sort: open failed: test_fusioncatcher/summary_candidate_fusions.txt: No such file or directory
ndaniel commented 7 years ago

Hi,

running the test on my laptop (quad-core, 24 GB RAM) takes 7 minutes. Therefore I think that something is going wrong in your case.

Would be possible to get the log of your run, which is the file /mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/test/test_fusioncatcher/fusioncatcher.log which contains all the commands executed by FusionCatcher and their execution times?

Currently my best guess is that it might be related to this https://github.com/alexdobin/STAR/issues/226 (and this is related to /lib/x86_64-linux-gnu/libc.so.6 which was mentioned already in the above posts). Therefore running this command maybe will fix this: 

cp -f /mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/tools/star/bin/Linux_x86_64_static/STAR  /mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/tools/star/source/

which would force FusionCatcher to use the statically linked executable of STAR instead of the dynamically linked executable.

Cheers, Daniel

ndaniel commented 7 years ago

I looked into this more and now I believe more than this might fix it:

cp -f \
/mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/tools/star/bin/Linux_x86_64_static/STAR \
/mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/tools/star/source/

Afterwards just re-run ./test.sh.

komalsrathi commented 7 years ago

Hi,

Please see the log file of the test /mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/test/test_fusioncatcher/fusioncatcher.log: https://drive.google.com/open?id=0B-8gQV1WZcYdNnVQaHZIUDg0bjQ

As you can see, there is nothing under fusioncatcher_v0.99.7b, this is the directory structure of /mnt/isilon/cbmi/variome/bin/fusioncatcher/fusioncatcher_v0.99.7b/:

./
|-- AUTHORS
|-- DEPENDENCIES
|-- LICENSE
|-- NEWS
|-- README.md
|-- VERSION
|-- bin
|   |-- FC
|   |-- add_ambiguous_counts.py
|   |-- add_custom_gene.py
|   |-- analyze_exon-exon_mappings.py
|   |-- analyze_splits_sam.py
|   |-- analyze_star_chimeric.py
|   |-- biopython_version.py
|   |-- blat-filter-fusion.py
|   |-- blat-filter-fusion.sh
|   |-- blat_parallel.py
|   |-- bootstrap.py
|   |-- build.sh
|   |-- build_ig.py
|   |-- build_report_fusions_map.py
|   |-- build_report_fusions_psl.py
|   |-- build_summary.py
|   |-- clean_bed.py
|   |-- clip_quality.py
|   |-- compress-reads-ids.py
|   |-- concatenate.py
|   |-- configuration.py
|   |-- configuration.pyc
|   |-- convert_pairs_symbols.py
|   |-- download-data-human.sh
|   |-- download.sh
|   |-- enlarge_genes.py
|   |-- extract_fusion_genes.py
|   |-- extract_reads_ids.py
|   |-- extract_short_reads.py
|   |-- extract_transcripts.py
|   |-- fasta2reads.py
|   |-- fastq2fasta.py
|   |-- fastq_b2n.py
|   |-- find_fusion_genes_map.py
|   |-- find_fusion_genes_psl.py
|   |-- find_homolog_genes.py
|   |-- fix.py
|   |-- fragment_fastq.py
|   |-- fragments_fusion_genes.py
|   |-- fusioncatcher
|   |-- fusioncatcher-batch
|   |-- fusioncatcher-batch.py
|   |-- fusioncatcher-build
|   |-- fusioncatcher-build.py
|   |-- fusioncatcher.py
|   |-- generate_1000genomes.py
|   |-- generate_18cancers.py
|   |-- generate_adjacent_genes.py
|   |-- generate_banned.py
|   |-- generate_bodymap2.py
|   |-- generate_chrom_lens.py
|   |-- generate_enlarge.py
|   |-- generate_exon-exon_junctions.py
|   |-- generate_exons.py
|   |-- generate_gene-gene_junctions.py
|   |-- generate_genes.py
|   |-- generate_genes_symbols.py
|   |-- generate_genes_with_no_proteins.py
|   |-- generate_gliomas.py
|   |-- generate_healthy.py
|   |-- generate_hpa.py
|   |-- generate_known.py
|   |-- generate_labels_descriptions.py
|   |-- generate_nontumor.py
|   |-- generate_oesophagus.py
|   |-- generate_overlapping_genes.py
|   |-- generate_pairs_pseudogenes.py
|   |-- generate_rrna_unit.py
|   |-- generate_tcga.py
|   |-- generate_transcripts.py
|   |-- get_biotypes.py
|   |-- get_cacg.py
|   |-- get_celllines.py
|   |-- get_cgp.py
|   |-- get_chimerdb2.py
|   |-- get_chimerdb3.py
|   |-- get_conjoing.py
|   |-- get_cosmic.py
|   |-- get_dgd.py
|   |-- get_exons_positions.py
|   |-- get_gencode.py
|   |-- get_genes_descriptions.py
|   |-- get_genome.py
|   |-- get_gtex.py
|   |-- get_gtf.py
|   |-- get_hla.py
|   |-- get_mtrna.py
|   |-- get_noncancer.py
|   |-- get_pancreases.py
|   |-- get_paralogs.py
|   |-- get_phix174.py
|   |-- get_prostates.py
|   |-- get_refseq.py
|   |-- get_refseq_ensembl.py
|   |-- get_rrna.py
|   |-- get_synonyms.py
|   |-- get_ticdb.py
|   |-- get_trna.py
|   |-- get_ucsc.py
|   |-- get_viruses.py
|   |-- join_homolog_genes.py
|   |-- label_ambiguous_fusion_genes.py
|   |-- label_found_fusions.py
|   |-- label_fusion_genes.py
|   |-- lengths_reads.py
|   |-- liftover.py
|   |-- mega.sh
|   |-- merge-sam.py
|   |-- merge_reports.py
|   |-- overlap.py
|   |-- padding-fastq.py
|   |-- pair8removal.py
|   |-- phred.py
|   |-- phred.pyc
|   |-- predict_frame.py
|   |-- psl_best_unique_contigs.py
|   |-- python_version.py
|   |-- reads_from_map.py
|   |-- remove-adapter.py
|   |-- remove-bad-illumina.py
|   |-- remove_custom_feature.py
|   |-- remove_reads_exon_exon_fastq.py
|   |-- remove_reads_exon_exon_map.py
|   |-- remove_reads_exon_exon_psl.py
|   |-- remove_reads_genome_transcriptome.py
|   |-- remove_shorter_reads.py
|   |-- remove_str.py
|   |-- sam2psl.py
|   |-- seqtk-subseq.sh
|   |-- shield_genes.py
|   |-- shuffle.py
|   |-- smoothing_fusions_psl.py
|   |-- solexa18to15.py
|   |-- sort_ttdb.py
|   |-- sort_ttdb.pyc
|   |-- split-fasta.py
|   |-- split-reads.py
|   |-- sra2illumina.py
|   |-- symbols.py
|   |-- trim_poly_tails.py
|   |-- trim_reads.py
|   |-- workflow.py
|   `-- workflow.pyc
|-- custom_install.sh
|-- doc
|   `-- manual.md
|-- etc
|   `-- configuration.cfg
|-- test
|   |-- final-list_candidate-fusion-genes.txt
|   |-- readme.txt
|   |-- reads_1.fq.gz
|   |-- reads_2.fq.gz
|   |-- summary_candidate_fusions.txt
|   |-- test.sh
|   `-- test_fusioncatcher
`-- tools

Also, this is my etc/configuration.cfg file:

$ cat etc/configuration.cfg 
[paths]
python = /usr/bin
data = /mnt/isilon/cbmi/variome/bin/fusioncatcher/data/current
scripts = /mnt/isilon/cbmi/variome/bin/fusioncatcher/bin
bowtie = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/bowtie
bowtie2 = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/bowtie2
bwa = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/bwa
blat = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/blat
liftover = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/liftover
star = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/star/source
velvet = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/velvet
fatotwobit = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/fatotwobit
samtools = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/samtools
seqtk = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/seqtk
sra = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/sratoolkit/bin
numpy = /usr/lib64/python2.6/site-packages/numpy
biopython = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/biopython
xlrd = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/xlrd
openpyxl = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/openpyxl
lzo = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/lzo
lzop = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/lzop/src
coreutils = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/coreutils/src
pigz = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/pigz
pxz = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/pxz
picard = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/picard
parallel = /mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/parallel/src
java = /usr/bin/

[parameters]
threads = 0
aligners = blat,star

[versions]
fusioncatcher = 0.99.7b beta

Does fusioncatcher pick up the installations from this file? Because I do have another STAR installation - do you think that could be a problem?

$ which STAR
/mnt/isilon/cbmi/variome/bin/STAR
ndaniel commented 7 years ago

Does this fix it?

cp -f \
/mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/star/bin/STAR \
/mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/star/source/
komalsrathi commented 7 years ago

Awesome! Got it to work in 8 mins and the installation is ok! Thanks for being so prompt in replying.

ndaniel commented 7 years ago

Great! I had a typo in the above fix, where it should have been this:

cp -f \
/mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/star/bin/Linux_x86_64_static/STAR \
/mnt/isilon/cbmi/variome/bin/fusioncatcher/tools/star/source/

I guess that you figured it out anyway!

Another comment it that the installation of FusionCatcher is a little bit uncommon and I do not know if this is due to some bug in bootstrap.py or is something else. Anyway the installation is uncommon but it works.

komalsrathi commented 7 years ago

Yeah I forgot to mention that I figured out the Linux_x86_64_static part. Yeah it took a while but it works!