Question: Using rmats on bioconda
0
gravatar for gcottone
19 months ago by
gcottone0
gcottone0 wrote:

Hi I am new to using both rmats as well as the bioconda system. I am curious as to if I put the same input into the line in conda as I would on rmats, i.e.;

"python RNASeq-MATS.py -b1 testData/231ESRP.25K.rep-1.bam,testData/231ESRP.25K.rep-2.bam -b2 testData/231EV.25K.rep-1.bam,testData/231EV.25K.rep-2.bam -gtf gtf/Homo_sapiens.Ensembl.GRCh37.72.gtf -o bam_test -t paired -len 50 -c 0.0001 -analysis U -libType fr-firststrand"

What should I change to start getting output?

thanks

rna-seq • 1.0k views
ADD COMMENTlink modified 19 months ago by Arup Ghosh2.8k • written 19 months ago by gcottone0

I think your question is not directly related to bioinformatics. However, I would try which python . If python is available from your bioconda --> ~/anaconda3/bin/python, then command will run otherwise no. Then you may need to do conda activate

ADD REPLYlink written 19 months ago by Prakash2.1k

Ok, I am just curious if you have any recommendations to other forums that may be able to help more? Since this isn't directly related to bioinformatics

ADD REPLYlink written 19 months ago by gcottone0
0
gravatar for WouterDeCoster
19 months ago by
Belgium
WouterDeCoster45k wrote:

Conda is just the package manager, it doesn't really* change how you execute the software.

*to be technically correct: for e.g. Java tools a wrapper script is used, so the name of the executable can be different

ADD COMMENTlink written 19 months ago by WouterDeCoster45k
0
gravatar for Arup Ghosh
19 months ago by
Arup Ghosh2.8k
India
Arup Ghosh2.8k wrote:

Assuming that you have installed rmats 4.0.2 using the bioconda channel and using Anaconda2 (as the tool requires python 2.7) the RNASeq-MATS.py script will be available in ~/anaconda2/bin/. Also, the tool is looking for text inputs in -b1 and -b2 as per the tool documentation, not sure if the command-line input will work. So a working command-line will look like the following example.

~/anaconda2/bin/python ~/anaconda2/bin/RNASeq-MATS.py --b1 b1.txt --b2 b2.txt --gtf gtfFile --od outDir -t readType --nthread nthread --readLength readLength
ADD COMMENTlink modified 19 months ago • written 19 months ago by Arup Ghosh2.8k
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