Closed jackhump closed 6 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 $paired variable is unbound. I got to the point where Step1a and Step1b submit but then due to wanting to go home on a Friday I used git checkout to roll my local version of the pipeline back to an older version (d1932e5 https://github.com/plagnollab/RNASeq_pipeline/commit/d1932e57bfb025be605fe6e157d2b0f2a7f5e0e2) and ran it. All the steps submitted. I guess we'll fix this on Monday.
— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/12.
Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol Lab blog: http://plagnol-lab.blogspot.co.uk/
What exactly are you running can you send the path to your script. Will fix tomorrow.
On Friday, 4 December 2015, Vincent Plagnol notifications@github.com wrote:
So all they say is true? It is actually possible to checkout an old version of a git repo?
On Fri, Dec 4, 2015 at 6:03 PM, Jack Humphrey <notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote:
I've been trying to run this dataset through the RNAseq pipeline. Here are my conditions from the support file: export RNASEQPIPBASE=$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 $paired variable is unbound. I got to the point where Step1a and Step1b submit but then due to wanting to go home on a Friday I used git checkout to roll my local version of the pipeline back to an older version (d1932e5 < https://github.com/plagnollab/RNASeq_pipeline/commit/d1932e57bfb025be605fe6e157d2b0f2a7f5e0e2 ) and ran it. All the steps submitted. I guess we'll fix this on Monday.
— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/12.
Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol Lab blog: http://plagnol-lab.blogspot.co.uk/
— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/12#issuecomment-162052317 .
And no there is no scoping in bash all variables are global.
On Friday, 4 December 2015, Vincent Plagnol notifications@github.com wrote:
So all they say is true? It is actually possible to checkout an old version of a git repo?
On Fri, Dec 4, 2015 at 6:03 PM, Jack Humphrey <notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote:
I've been trying to run this dataset through the RNAseq pipeline. Here are my conditions from the support file: export RNASEQPIPBASE=$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/
— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/12#issuecomment-162052317 .
Yes Vincent it's true, Chris showed me. It was glorious. I managed to leave work on time.
I just typed:
$ git checkout
and it reset my version to Monday's edition of the pipeline.
regards,
Jack
Jack Humphrey | PhD student
Institute of Neurology & UCL Genetics Institute | University College London
M: 07896 208 263
From: Nikolas Pontikos notifications@github.com Sent: 04 December 2015 19:07 To: plagnollab/RNASeq_pipeline Cc: Humphrey, Jack Subject: Re: [RNASeq_pipeline] Not working (#12)
And no there is no scoping in bash all variables are global.
On Friday, 4 December 2015, Vincent Plagnol notifications@github.com wrote:
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 javascript:_e(%7B%7D,'cvml','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 $paired variable is unbound. I got to the point where Step1a and Step1b submit but then due to wanting to go home on a Friday I used git checkout to roll my local version of the pipeline back to an older version (d1932e5 < https://github.com/plagnollab/RNASeq_pipeline/commit/d1932e57bfb025be605fe6e157d2b0f2a7f5e0e2 ) and ran it. All the steps submitted. I guess we'll fix this on Monday.
Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/12.
Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol Lab blog: http://plagnol-lab.blogspot.co.uk/
Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/12#issuecomment-162052317 .
Reply to this email directly or view it on GitHubhttps://github.com/plagnollab/RNASeq_pipeline/issues/12#issuecomment-162054739.
So the updated script is running now for step2, just pushed some fix to the repo.
On Fri, Dec 4, 2015 at 7:01 PM, Nikolas Pontikos notifications@github.com wrote:
What exactly are you running can you send the path to your script. Will fix tomorrow.
On Friday, 4 December 2015, Vincent Plagnol notifications@github.com wrote:
So all they say is true? It is actually possible to checkout an old version of a git repo?
On Fri, Dec 4, 2015 at 6:03 PM, Jack Humphrey <notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');>
wrote:
I've been trying to run this dataset through the RNAseq pipeline. Here are my conditions from the support file: export RNASEQPIPBASE=$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 $paired variable is unbound. I got to the point where Step1a and Step1b submit but then due to wanting to go home on a Friday I used git checkout to roll my local version of the pipeline back to an older version (d1932e5 <
https://github.com/plagnollab/RNASeq_pipeline/commit/d1932e57bfb025be605fe6e157d2b0f2a7f5e0e2
) and ran it. All the steps submitted. I guess we'll fix this on Monday.
— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/12.
Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol Lab blog: http://plagnol-lab.blogspot.co.uk/
— Reply to this email directly or view it on GitHub < https://github.com/plagnollab/RNASeq_pipeline/issues/12#issuecomment-162052317
.
— Reply to this email directly or view it on GitHub https://github.com/plagnollab/RNASeq_pipeline/issues/12#issuecomment-162053136 .
Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol
ok great thanks a lot Vincent and sorry again guys! Is it all good then? can we close this issue?
I've been trying to run this dataset through the RNAseq pipeline. Here are my conditions from the support file: export RNASEQPIPBASE=$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.