| Previous changeset 47:9ba44c15cad1 (2019-06-18) Next changeset 49:df3645fb1bc0 (2019-07-10) |
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Commit message:
Uploaded |
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modified:
complete_immunerepertoire.xml report_clonality/r_wrapper.sh |
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added:
report_clonality/circos/etc/LTe50046.ttf report_clonality/circos/etc/LTe50048.ttf report_clonality/circos/etc/LTe50050.ttf report_clonality/circos/etc/LTe50054.ttf report_clonality/circos/etc/pragmata.ttf report_clonality/circos/etc/wingding.ttf |
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| diff -r 9ba44c15cad1 -r efe0a2b5d163 complete_immunerepertoire.xml --- a/complete_immunerepertoire.xml Tue Jun 18 05:28:11 2019 -0400 +++ b/complete_immunerepertoire.xml Tue Jun 18 09:23:41 2019 -0400 |
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| @@ -7,6 +7,7 @@ <requirement type="package" version="1.4.3">r-reshape2</requirement> <requirement type="package" version="1.3.0">r-lymphclon</requirement> <requirement type="package" version="0.69.6">circos</requirement> + <requirement type="package" version="0.23">circos-tools</requirement> </requirements> <description> </description> <command interpreter="bash"> |
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| diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/LTe50046.ttf |
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| diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/LTe50048.ttf |
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| diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/LTe50050.ttf |
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| diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/LTe50054.ttf |
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| diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/pragmata.ttf |
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| diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/wingding.ttf |
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| diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/r_wrapper.sh --- a/report_clonality/r_wrapper.sh Tue Jun 18 05:28:11 2019 -0400 +++ b/report_clonality/r_wrapper.sh Tue Jun 18 09:23:41 2019 -0400 |
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| @@ -59,34 +59,12 @@ echo "<html><head><title>Report on:" >> $outputFile mkdir $outputDir/circos -cp $dir/circos/* $outputDir/circos/ -#CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" -#CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" - -#CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools" -#CIRCOSDIR="/home/galaxy/Anaconda3/bin" +cp -R $dir/circos/* $outputDir/circos/ USECIRCOS="no" -if [ -d "$CIRCOSDIR" ]; then +path_to_circos=$(which circos) +if [ -x "$path_to_circos" ]; then USECIRCOS="yes" -else - if [ -d "/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" ]; then #hopefully temporary fix - USECIRCOS="yes" - CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" - CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" - fi - - if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix #or not - USECIRCOS="yes" - CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools" - CIRCOSDIR="/home/galaxy/Anaconda3/bin" - fi - - if [ -d "/media/galaxy/data/other_backup/circos/galaxian-circos//bin" ]; then #hopefully temporary fix #or not #really not - USECIRCOS="yes" - CIRCOSTOOLS="/media/galaxy/data/other_backup/circos/galaxian-circos/tools" - CIRCOSDIR="/media/galaxy/data/other_backup/circos/galaxian-circos/bin" - fi fi echo "Using Circos: $USECIRCOS" @@ -102,12 +80,12 @@ sed -i -- 's%/%:%g' $circos_file echo -e -n "labels$(cat ${circos_file})" > ${circos_file} echo "Circos tools command:" - echo "cat \"${circos_file}\" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/" - cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ + echo "cat \"${circos_file}\" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/" + cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/ echo "Circos command:" - echo "$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1" - $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 + echo "circos -conf $outputDir/circos/circos.conf 2>&1" + circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg @@ -116,18 +94,18 @@ circos_file="$outputDir/${sample}_VD_circos.txt" sed -i -- 's%/%:%g' $circos_file echo -e -n "labels$(cat ${circos_file})" > ${circos_file} - cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ + cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/ sed -i -- 's%/%:%g' $outputDir/circos/cells.txt - $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 + circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg circos_file="$outputDir/${sample}_DJ_circos.txt" sed -i -- 's%/%:%g' $circos_file echo -e -n "labels$(cat ${circos_file})" > ${circos_file} - cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ + cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/ sed -i -- 's%/%:%g' $outputDir/circos/cells.txt - $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 + circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg fi |