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bcbio / bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
MIT License
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wrong url #7

Closed kspham closed 10 years ago

kspham commented 10 years ago

Seems that we have wrong url for snpEff database

bcbio_vm.py --datadir=~/install/bcbio-vm/data install --data --tool

Sourceforce is temporary down

[2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: oudbiolinux/e0181283-855a-3004-8cce-d1cc0bb01f2a [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: pwd [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: echo $HOME [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: mkdir -p '/root/tmp/cloudbiolinux/1dc34bd8-5448-3bc9-803d-443bd56fa501' [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: wget --continue --no-check-certificate -O cosmic-v68-GRCh37.vcf.gz.tbi 'https://s3.amazonaws.com/biodata/variants/cosmic-v68-GRCh37.vcf.gz.tbi' [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: mv cosmic-v68-GRCh37.vcf.gz.tbi /usr/local/share/bcbio-nextgen/genomes/Hsapiens/GRCh37/variation [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: rm -rf /root/tmp/cloudbiolinux/1dc34bd8-5448-3bc9-803d-443bd56fa501 [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: pwd [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: echo $HOME [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: mkdir -p '/root/tmp/cloudbiolinux/2e9e57b4-08e6-3871-bb91-2958e5de9928' [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: wget --continue --no-check-certificate -O human.hg19.excl.tsv 'https://raw.githubusercontent.com/chapmanb/delly/master/human.hg19.excl.tsv' [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: grep -v ^chr human.hg19.excl.tsv > sv_repeat_telomere_centromere.bed [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: mv sv_repeat_telomere_centromere.bed /usr/local/share/bcbio-nextgen/genomes/Hsapiens/GRCh37/variation [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: rm -rf /root/tmp/cloudbiolinux/2e9e57b4-08e6-3871-bb91-2958e5de9928 [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: pwd [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: echo $HOME [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: mkdir -p '/root/tmp/cloudbiolinux/3ada5782-1941-392d-96f1-ebf010bfd422' [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: wget --continue --no-check-certificate -O LCR-hs37d5.bed.gz 'https://github.com/lh3/varcmp/raw/master/scripts/LCR-hs37d5.bed.gz' [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: zcat LCR-hs37d5.bed.gz | bgzip -c > LCR.bed.gz [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: mv LCR.bed.gz /usr/local/share/bcbio-nextgen/genomes/Hsapiens/GRCh37/variation [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: rm -rf /root/tmp/cloudbiolinux/3ada5782-1941-392d-96f1-ebf010bfd422 [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: [localhost] local: tabix -p vcf -f LCR.bed.gz [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: Updating GRCh37 genome resources configuration [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: Installing snpEff database GRCh37.75 in /usr/local/share/bcbio-nextgen/genomes/Hsapiens/GRCh37/snpeff [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: Traceback (most recent call last): [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: File "/usr/local/bin/bcbio_nextgen.py", line 45, in [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: install.upgrade_bcbio(kwargs["args"]) [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/install.py", line 66, in upgrade_bcbio [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: upgrade_bcbio_data(args, REMOTES) [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/install.py", line 159, in upgrade_bcbio_data [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: _upgrade_snpeff_data(s["fabricrc_overrides"]["galaxy_home"], args, remotes) [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/install.py", line 211, in _upgrade_snpeff_data [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: subprocess.check_call(["wget", "-c", "-O", dl_file, dl_url]) [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/subprocess.py", line 540, in check_call [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: raise CalledProcessError(retcode, cmd) [2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout: subprocess.CalledProcessError: Command '['wget', '-c', '-O', 'snpEff_v3_4_GRCh37.75.zip', 'http://downloads.sourceforge.net/project/snpeff/databases/v3_4/snpEff_v3_4_GRCh37.75.zip']' returned non-zero exit status 8

chapmanb commented 10 years ago

Son; Apologies about the problem, the docker image was out of date and didn't have the latest snpEff needed to get the Ensembl 75 databases. I updated the image, so if you re-run the install command it should grab the latest image and work cleanly now. Thanks again for the report.