Public | Automated Build

Last pushed: 7 months ago
Short Description
specL based workflow
Full Description

generateSpecLibrary

develop best praxis

the default docker image is auto build and available through https://hub.docker.com/r/cpanse/generatespeclibrary/

lets assume you want to change the Rmd file.

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

try run

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

submit a real job

application:
  input:
    mascot_dat:
    - bfabric@fgcz-r-018.uzh.ch://usr/local/mascot//data/20170117/F246914.dat
    - bfabric@fgcz-r-018.uzh.ch://usr/local/mascot//data/20170113/F246713.dat
    - bfabric@fgcz-r-018.uzh.ch://usr/local/mascot//data/20170113/F246709.dat
    - bfabric@fgcz-r-018.uzh.ch://usr/local/mascot//data/20170113/F246708.dat
    - bfabric@fgcz-r-018.uzh.ch://usr/local/mascot//data/20170113/F246711.dat
    - bfabric@fgcz-r-018.uzh.ch://usr/local/mascot//data/20170113/F246710.dat
  output:
  - bfabric@fgczdata.fgcz-net.unizh.ch:/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
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