cpanse/generatespeclibrary repository overview

git clone https://github.com/fgcz/generateSpecLibrary \
&& cd generateSpecLibrary \
&& mkdir tmp \
&& cd tmp \
&& cp ../specL.Rmd .

[ $? -eq 0 ] && echo -e "FROM cpanse/generatespeclibrary\nADD specL.Rmd /usr/local/src\n" \
> Dockerfile
[ $? -eq 0 ] && docker build .

# Have Fun
docker run -ti -v/scratch/generatespeclibrary/:/scratch/generatespeclibrary/ \
	-v /usr/local/mascot/data:/usr/local/mascot/data \
	-v /usr/local/mascot/sequences:/usr/local/mascot/sequences \
	$DOCKERIMAGEID bash

docker pull cpanse/generatespeclibrary

docker run -it -v/scratch/generatespeclibrary/:/scratch/generatespeclibrary/ \
	-v /usr/local/mascot/data:/usr/local/mascot/data \
	-v /usr/local/mascot/sequences:/usr/local/mascot/sequences \
	cpanse/generatespeclibrary bash

application:
  input:
    mascot_dat:
    - [email protected]://usr/local/mascot//data/20170117/F246914.dat
    - [email protected]://usr/local/mascot//data/20170113/F246713.dat
    - [email protected]://usr/local/mascot//data/20170113/F246709.dat
    - [email protected]://usr/local/mascot//data/20170113/F246708.dat
    - [email protected]://usr/local/mascot//data/20170113/F246711.dat
    - [email protected]://usr/local/mascot//data/20170113/F246710.dat
  output:
  - [email protected]:/srv/www/htdocs//p2290/bfabric/Proteomics/DIA_Assay_Library_Generator/2017/2017-03/2017-03-28//workunit_153227//359697.zip
  parameters:
    mascot_database_location: /usr/local/mascot/sequence/
    maxN: '6'
    minN: '5'
    mzError: '0.05'
  protocol: scp

docker run -it \
	-v/scratch/generatespeclibrary/:/scratch/generatespeclibrary/ \
	-v /usr/local/mascot/data:/usr/local/mascot/data \
	-v /misc/mascotsequence/:/usr/local/mascot/sequence cpanse/generatespeclibrary \
	fgcz_AssayLibraryGeneration.py config.3121.yaml