cosmid
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robinandeer
Genomics database manager
It seems the dependency for path.py doesn't require a specific version and path.py beyond version 8 (I have not confirmed yet) is causing the following problem. ``` $ cosmid Traceback...
ccds: ftplib.error_temp: 450 pub/CCDS/archive/Hs106: No such file or directory ftplib.error_perm: 550 bundle/2.8/b37/dbsnp_137.b37.excluding_sites_after_129.vcf.gz: No such file or directory
Stödjer cosmid annat än ftp nedladdnigar? Jag skulle behöva kunna tanka ner följande filer via cosmid till MIP och visa är riktigt stora: http://evs.gs.washington.edu/evs_bulk_data/ESP6500SI-V2-SSA137.protein-hgvs-update.snps_indels.vcf.tar.gz http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFPv2.4.zip http://krishna.gs.washington.edu/download/CADD/v1.0/whole_genome_SNVs.tsv.gz http://krishna.gs.washington.edu/download/CADD/v1.0/whole_genome_SNVs.tsv.gz.tbi http://krishna.gs.washington.edu/download/CADD/v1.0/1000G.tsv.gz http://krishna.gs.washington.edu/download/CADD/v1.0/1000G.tsv.gz.tbi
Cool stuff @robinandeer, as always! Cosmid really reminds me of git-annex, have you checked it out? People over here in #neuro (@yarikoptic) are going for DataGit: https://github.com/data-git/datagit Let me know...
New alternative implementation of essentially what cosmid is trying to accomplish: https://github.com/jbenet/data - \+ Compiled binaries - \+ Generalized (larger potential community)
GATK bundle resources get error and die Retry 5 times with timeout instead
Hej Robin, jag experimenterar lite med cosmid. Mycket trevlig idé. Hur är det med namnet på dbsnp-filen? Det verkar låst till dbsnp_137 även när källan är v138? Bug eller feature?...