Mercurial > repos > mvdbeek > igv_take_screenshots
changeset 32:9382c8499e73 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit c6f25b122899a00695b5ca9e70d34e2c1d288236-dirty
| author | mvdbeek |
|---|---|
| date | Sun, 20 Jan 2019 14:30:27 -0500 |
| parents | 474837e086cc |
| children | 3f980046df62 |
| files | Dockerfile igv_make_screenshots.xml xvfb_igv.py |
| diffstat | 3 files changed, 2 insertions(+), 19 deletions(-) [+] |
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--- a/Dockerfile Sun Jan 20 13:30:21 2019 -0500 +++ b/Dockerfile Sun Jan 20 14:30:27 2019 -0500 @@ -1,4 +1,4 @@ FROM continuumio/miniconda3:4.5.11 RUN apt-get update && apt-get install -y xvfb libxrender1 libxtst6 && apt-get clean -RUN conda create -p /usr/local --copy -y -c conda-forge -c bioconda xvfbwrapper samtools igv openjdk=8 freetype font-ttf-dejavu-sans-mono fontconfig coreutils && rm -Rf /opt +RUN conda install -y -c conda-forge -c bioconda xvfbwrapper samtools igv openjdk=8 freetype font-ttf-dejavu-sans-mono fontconfig coreutils
--- a/igv_make_screenshots.xml Sun Jan 20 13:30:21 2019 -0500 +++ b/igv_make_screenshots.xml Sun Jan 20 14:30:27 2019 -0500 @@ -51,7 +51,7 @@ cat load_session.txt '$script_file' '$exit_session' > igv_script.txt && cp '$igv_session_remote' '$igv_session_out' #if not $skip_screenshots: - && python $__tool_directory__/xvfb_igv.py igv_script.txt '$igv_preferences' $width,$height && + && xvfb-run --server-args="-screen 0 ${width}x${height}x24" igv -g genome.fa -o '$igv_preferences' --batch igv_script.txt && mkdir screenshots && mv *.png screenshots #end if ]]></command>
--- a/xvfb_igv.py Sun Jan 20 13:30:21 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -import os -import subprocess -import sys - -import xvfbwrapper - - -def take_screenshots(igv_script, preferences_file, screensize): - width, height = screensize.split(',') - with xvfbwrapper.Xvfb(width=width, height=height) as xvfb: - exit_code = subprocess.call(['igv', '-g', 'genome.fa', '-o', preferences_file, '--batch', igv_script], env=os.environ.copy()) - sys.exit(exit_code) - - -if __name__ == '__main__': - take_screenshots(sys.argv[1], sys.argv[2], sys.argv[3]) -