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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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We should make sure RUM_runner can be run with relative paths #12

Closed mdelaurentis closed 12 years ago

mdelaurentis commented 12 years ago

Katerina ran the following command, and the qsub'ed jobs failed:

perl ~/Tools/RUM-1.11/bin/RUM_runner.pl ~/Tools/RUM-1.11/conf/rum.config_hg19 fwd.fq,,,rev.fq rum2/ 5 kat_test -qsub

She then ran this and it worked:

perl /gpfs/fs121/hts/Tools/RUM-1.11/bin/RUM_runner.pl /gpfs/fs121/hts/Tools/RUM-1.11/conf/rum.config_hg19 /gpfs/fs121/hts/RUM-1.11_test/fwd.fq,,,/gpfs/fs121/hts/RUM-1.11_test/rev.fq /gpfs/fs121/hts/RUM-1.11_test/rum3/ 5 kat_test -qsub

It seems that adding "-cwd" to the qsub commands would be a pretty simple fix; I'll take care of it for the next version.

khayer commented 12 years ago

Rum indexes seems to have a similar problem:

 root@master:/data/Tools/RUM-Pipeline-2.00_09# rum_indexes 
 Looking at the repository located at /data/Tools/rum/bin/..
 --------------------------------------------------------------------------------
 The following indexes are available.
 Indexes that you already have are marked with '*':

    1     hg19:                human (Homo sapiens)
    2     hg18:                human (Homo sapiens)
    3      mm9:                mouse (Mus musculus)
    4  danRer7:            zebrafish (Danio rerio)
    5      dm3:            fruit fly (Drosophila melanogaster)
    6  anoGam1:             mosquito (Anopheles gambiae)
    7      c36:        nematode worm (Caenorhabditis elegans)
    8  sacCer3:                yeast (Saccharomyces cerevisiae)
    9       m4:                  rat (Rattus norvegicus)
   10  susScr2:                  pig (Sus scrofa)
   11  canFam2:                  dog (Canis lupus familiaris)
   12  panTro2:           chimpanzee (Pan troglodytes)
   13  ponAbe2:            orangutan (Pongo pygmaeus abelii)
   14  rheMac2:        rhesus monkey (Macaca mulatta)
   15  galGal3:              chicken (Gallus gallus)
   16  06-2010:     malaria parasite (Plasmodium falciparum)
   17   TAIR10:          arabadopsis (Arabidopsis thaliana)

Enter the number of an index to install or q to quit: 8
I'll install sacCer3: yeast (Saccharomyces cerevisiae)
http://itmat.rum.s3.amazonaws.com/rum.config_saccer3
Error running wget -q -O /data/Tools/rum/bin/../conf/rum.config_saccer3 http://itmat.rum.s3.amazonaws.com/rum.config_saccer3:  at /data/Tools/rum/bin/rum_indexes line 293
mdelaurentis commented 12 years ago

RUM 2 should work fine with relative paths. I have installed indexes in relative paths, and I run jobs using relative paths quite often.