Mercurial > repos > mvdbeek > igv_take_screenshots
changeset 8:ff0fb6dde58e draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
| author | mvdbeek |
|---|---|
| date | Mon, 03 Jul 2017 10:58:06 -0400 |
| parents | 755832a07414 |
| children | c357862a2927 |
| files | igv_make_screenshots.xml test-data/complete_batchscript.txt |
| diffstat | 2 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/igv_make_screenshots.xml Mon Jul 03 10:03:17 2017 -0400 +++ b/igv_make_screenshots.xml Mon Jul 03 10:58:06 2017 -0400 @@ -6,7 +6,7 @@ #for $inputsection in $inputfiles #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension) sed -i.bak -e "s|$path|\$PWD/$path|g" '$igv_session' && - ln -fs $inputsection.input $path && + ln -fs '$inputsection.input' '$path' && #if $inputsection.input.is_of_type('bam') ln -fs $inputsection.input.metadata.bam_index '$path'.bai && #end if @@ -15,6 +15,7 @@ cat '$load_session' > load_session.txt && echo snapshotDirectory "\$PWD" >> load_session.txt && cat load_session.txt '$script_file' '$exit_session' > igv_script.txt && + sleep 10s && python $__tool_directory__/xvfb_igv.py igv_script.txt $width,$height && cp '$igv_session' '$igv_session_out' && zip screenshots.zip *.png &&
--- a/test-data/complete_batchscript.txt Mon Jul 03 10:03:17 2017 -0400 +++ b/test-data/complete_batchscript.txt Mon Jul 03 10:58:06 2017 -0400 @@ -1,2 +1,2 @@ -goto 2R:18158676-7052469 -snapshot 2R_rover_18158676_7052469_slop300.png +goto 2R:7050658-7051658 +snapshot 2R_rover_7050658_7051658_slop300.png