vplagnol
commented
8 years ago So all they say is true? It is actually possible to checkout an old version of a git repo?
On Fri, Dec 4, 2015 at 6:03 PM, Jack Humphrey notifications@github.com wrote:
I've been trying to run this dataset through the RNAseq pipeline. Here are my conditions from the support file: export RNASEQPIPBASE=$RNASEQPIPBASE export RNASEQBUNDLE=$RNASEQBUNDLE pipeline=${RNASEQPIPBASE}/RNAseq_pipeline_v8.sh
############# species=human_hg38 submit=yes force=yes
QC=yes starStep1a=yes starStep1b=yes starStep2=yes
summary=yes prepareCounts=yes Rdeseq=yes Rdexseq=yes
oFolder=/cluster/scratch3/vyp-scratch2/Humphrey_datasets/TDP_ENCODE/dataset_2/processed
iFolder=/cluster/scratch3/vyp-scratch2/Humphrey_datasets/TDP_ENCODE/dataset_2/
dataframe=${iFolder}/encode_tdp_2_support.tab code=encode_dataset1
sh $pipeline --QC ${QC} --iFolder ${iFolder} --oFolder ${oFolder} --dataframe ${dataframe} --code ${code} --prepareCounts ${prepareCounts} --Rdexseq ${Rdexseq} --Rdeseq ${Rdeseq} --summary ${summary} --starStep1a ${starStep1a} --starStep1b ${starStep1b} --starStep2 ${starStep2} --species ${species} --submit ${submit} --force ${force}
At first it was stopping because of typos (file_exists vs files_exist) and then it was stopping because of unbounded variables (finalOfolder, does it have to be defined at every function again Niko? I've now declared it within every function and that error disappeared) and then finally the $paired variable is unbound. I got to the point where Step1a and Step1b submit but then due to wanting to go home on a Friday I used git checkout to roll my local version of the pipeline back to an older version (d1932e5 https://github.com/plagnollab/RNASeq_pipeline/commit/d1932e57bfb025be605fe6e157d2b0f2a7f5e0e2) and ran it. All the steps submitted. I guess we'll fix this on Monday.
— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/12.
Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol Lab blog: http://plagnol-lab.blogspot.co.uk/
pontikos
jackhump
I've been trying to run this dataset through the RNAseq pipeline. Here are my conditions from the support file: export RNASEQPIPBASE=$RNASEQPIPBASE export RNASEQBUNDLE=$RNASEQBUNDLE pipeline=${RNASEQPIPBASE}/RNAseq_pipeline_v8.sh
species=human_hg38 submit=yes force=yes
QC=yes starStep1a=yes starStep1b=yes starStep2=yes
summary=yes prepareCounts=yes Rdeseq=yes Rdexseq=yes
oFolder=/cluster/scratch3/vyp-scratch2/Humphrey_datasets/TDP_ENCODE/dataset_2/processed iFolder=/cluster/scratch3/vyp-scratch2/Humphrey_datasets/TDP_ENCODE/dataset_2/
dataframe=${iFolder}/encode_tdp_2_support.tab code=encode_dataset1
sh $pipeline --QC ${QC} --iFolder ${iFolder} --oFolder ${oFolder} --dataframe ${dataframe} --code ${code} --prepareCounts ${prepareCounts} --Rdexseq ${Rdexseq} --Rdeseq ${Rdeseq} --summary ${summary} --starStep1a ${starStep1a} --starStep1b ${starStep1b} --starStep2 ${starStep2} --species ${species} --submit ${submit} --force ${force}
At first it was stopping because of typos (file_exists vs files_exist) and then it was stopping because of unbounded variables (finalOfolder, does it have to be defined at every function again Niko? I've now declared it within every function and that error disappeared) and then finally the $paired variable is unbound. I got to the point where Step1a and Step1b submit but then due to wanting to go home on a Friday I used git checkout to roll my local version of the pipeline back to an older version (d1932e57bfb025be605fe6e157d2b0f2a7f5e0e2) and ran it. All the steps submitted. I guess we'll fix this on Monday.