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apeltzer / ReportTable

The Report Generation Engine for the EAGER Pipeline
GNU General Public License v3.0
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Provide version information #17

Closed apeltzer closed 7 years ago

apeltzer commented 7 years ago

Please add a parameter to the program call (optional!):

--version or -version (or add the version to -h, so I can parse it)

apeltzer commented 7 years ago

EAGER-CLI v1.92.54 will produce output like this in the main folder of each sample:

GATK Version:
Picked up JAVA_TOOL_OPTIONS: -Djava.io.tmpdir=/home/peltzer/palshare/peltzer/2017-05-18_Thesis_Runs_Peltzer/EAGER_Evaluation/Syph_Modern_WGS/S7/0-FastQC/.tmp
nightly-2017-07-11-g1f763d5
Java Version:
openjdk version "1.8.0_131"
DeDup Version:
DeDup v0.12.1
AdapterRemoval Version:
AdapterRemoval ver. 2.2.1a
ClipAndMerge Version:
ClipAndMerge (v. 1.7.6)
CircularMapper Version:
usage: RealignSAMFilev1.0
FastQC version:
FastQC v0.11.5
Preseq Version:
Version: 2.0.1
VCF2Genome Version:
VCF2Genome (v. 0.91 2017-01-13)
BWA Version:
Version: 0.7.15-r1140
mapDamage Version:
2.0.6
GNU R Version:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Bowtie2 Version:
/usr/bin/bowtie2-align-s version 2.3.2
ANGSD Version:
       -> angsd version: 0.917-104-g5f2c254 (htslib: 1.4) build(Mar 24 2017 10:10:39)

This should make it feasible to integrate that with the report. It would be great to have this in the ReportTable, too.

alex-seitz commented 7 years ago

The ReportTable now prints its version number on every start