# HG changeset patch
# User mvdbeek
# Date 1501260425 14400
# Node ID 1100d5a77c4d80613d7d3add9209cb5059965112
# Parent 9dca6aa224a226ba14885dcdd0f507c0b86694a1
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1ddb87e95baeea2a4ee9b95930da6e0927fb7ff7-dirty
diff -r 9dca6aa224a2 -r 1100d5a77c4d igv_make_screenshots.xml
--- a/igv_make_screenshots.xml Mon Jul 03 12:40:16 2017 -0400
+++ b/igv_make_screenshots.xml Fri Jul 28 12:47:05 2017 -0400
@@ -1,11 +1,15 @@
xvfbwrapper
+ igv
load_session.txt &&
echo snapshotDirectory "\$PWD" >> load_session.txt &&
cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
- ## gives the cluster a bit of time to actually create the symlinks ... ughs
- sleep 10s &&
+ cp '$igv_session' '$igv_session_out' &&
python $__tool_directory__/xvfb_igv.py igv_script.txt '$igv_preferences' $width,$height &&
- cp '$igv_session' '$igv_session_out' &&
zip screenshots.zip *.png &&
cp screenshots.zip '$screenshots_out'
]]>
-
-
+
+
- #for $inputsection in $inputfiles
- #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
+ #for $i, $inputsection in enumerate($inputfiles):
+ #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)
#set $coverage_id="%s_coverage" % $path
#end for
- #for $inputsection in $inputfiles
+ #for $i, $inputsection in enumerate($inputfiles):
#if $inputsection.input.is_of_type('bam')
#set $label=str($inputsection.label) if str($inputsection.label) else str($inputsection.input.element_identifier)
- #set $path="%s.%s" % ($inputsection.input.element_identifier, $inputsection.input.extension)
+ #set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)
## First track is the coverage
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@@ -97,7 +107,22 @@
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+ 10.1093/bib/bbs017
+
diff -r 9dca6aa224a2 -r 1100d5a77c4d test-data/complete_batchscript.txt
--- a/test-data/complete_batchscript.txt Mon Jul 03 12:40:16 2017 -0400
+++ b/test-data/complete_batchscript.txt Fri Jul 28 12:47:05 2017 -0400
@@ -1,2 +1,2 @@
-goto 2R:7050658-7051658
-snapshot 2R_rover_7050658_7051658_slop300.png
+goto 2R:1-1551
+snapshot 2R_rover_1_1551_slop300.png
diff -r 9dca6aa224a2 -r 1100d5a77c4d test-data/igv_session.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/igv_session.xml Fri Jul 28 12:47:05 2017 -0400
@@ -0,0 +1,19 @@
+
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\ No newline at end of file
diff -r 9dca6aa224a2 -r 1100d5a77c4d test-data/rover_corrected.bam
Binary file test-data/rover_corrected.bam has changed
diff -r 9dca6aa224a2 -r 1100d5a77c4d test-data/rover_dont_split.bam
Binary file test-data/rover_dont_split.bam has changed
diff -r 9dca6aa224a2 -r 1100d5a77c4d test-data/rover_dont_split.bam.bai
Binary file test-data/rover_dont_split.bam.bai has changed
diff -r 9dca6aa224a2 -r 1100d5a77c4d test-data/rover_reference.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rover_reference.fa Fri Jul 28 12:47:05 2017 -0400
@@ -0,0 +1,31 @@
+>2R
+ATGTTTATATTGCGCCCTGTTCCCATCCCCCCACTGCCGCCAGAGCCTTCAATTGCTTTC
+ACCACCGCTCCCGCAGGATGATGTCATGTCCACGTACCCTCGCCCAGTATTCGCACTCTA
+GTTTGCAGTCTGACCTATATATCGCAATCGAACGCCGGAGTTTCCAAAACTGGGCCACCA
+ACGAGGGTGATTTGCCAACCCCCGGATGCGCGGGTATGGGAGTGAGGCGGAGGATTCATT
+TCATTATCACAGCGCTCAGTCAGGCAAACTTCCCGAACCACAAATTATGTGATGCACTCA
+GCTGCGGCTTTTAATTGCCACACAAATGAATGGCAATTGCCCTTGTAATTGCAACTGCAA
+CCGTATCATATTGTACAGGCGATCTTCTATAAGACCAACATTATATATGTATTTATTAGA
+AATTGAGGGATGTATTATTTGATTTAAGGATTCGATTCACCCATTAAATGTAAACGTTTC
+ATTAGATTAAGTTGTGAGTAATGTTCCTAAGTTCTAAAAGTCGATATAAGTATTCGATGC
+ACAGAGGTTTTACTGTCATAAATTTCAGTTTCTTGCTGCTGGGGCCATCGGCTGGATAGC
+TTACAATGCGGACACGGAGACGGAGGAATTCGTAATAGCCGCTTACATCGCGTGCTCGCT
+CATCCTGGTCTTTGCTCTGCTGGGCATCTTCGCGGCCATCCGGGAATCGGTGGTGCTGAC
+TGCAACGGTAGGCAATATAGTCAGGAAACCGTTTCTGAATTAACGCTGTTACGTATCCCT
+TAGAGTGCTGTCTTCCTGCTGATCTTGGCCATCCTGCAGATCGTGAGCACCTGCCTGTTC
+CTCCACGAGTTCGACGTGAAGAGCGGCCGGGACATGGTGGAGGTGGCCTGGCAGGCGAAC
+AACATGGATTCCTTGCAGCAGAAGCACGAGTGCTGCGGCCAGAGCAGCGCCCAGGACTAT
+ATCCACCTCAGCCTGCTGATCCCGCCCAGCTGCTACGCGGATCTGCAGCAGACCCCCGAC
+CACCTCTATCTGGACGGGTGCATCGAAAAGGTGCAGAGCTTCTACGAAAGCGACAAGCTG
+CGCTTCATCATAGTGTCCTGGGTGCTAGTGGCCTTCGAGGTGGGTTTTTCCTTAGCCCGA
+CTTAAGTACCAATATATTTAAATTAACCGACTTTCTTTCAGTTAATCTGCTTCGCCTTGG
+CCGTGTTTCTGGCCATTAGTTTTAAGAACAAGCAGCGACGGATGGAGTTCTAGTTCTAGG
+CCTTCGGTAATCTCGAGCTATCCAACAGTACAAACTCGGAATCGGGGTCTCGCTGATATT
+TTTCTCTTCAACATTTCATAACCAAATGCAAAGGACAGTCATAAATTATTCACTCCTACC
+TTAATGTAACCTGTAATTAAAGTACATATTTATAGTTCAATTACCCATTATAAGTATCAT
+AATAAATGTGCGCGTGTTTGTTTTCACATGATTTGCTCGCTTGTCAGTTTGTTTGTGTGT
+TCTGCCCGATGGAAATATTAAGCATACGACGCGTAGTCCCGACGAGCTTTGTATGGCCGA
+AACATTTCTCTATTTGCTTTGACTGCCAAATGACTTGTTGCTCGTCGCGTAATGGCATGC
+TTGGAATCTGTAGGGTTCCGTTAAGTGTGCGGCGCAGAAATATCTCAATGATGTCCTGTA
+ATCTATGATGTTAGTGCTCTGCGGTGGATGGATTTTGGTGGCCCCATTCAATTCCTAAAT
+AAAGAAAATGCGGTGAAAGCTTTAGCCGCTGTGACA
diff -r 9dca6aa224a2 -r 1100d5a77c4d xvfb_igv.py
--- a/xvfb_igv.py Mon Jul 03 12:40:16 2017 -0400
+++ b/xvfb_igv.py Fri Jul 28 12:47:05 2017 -0400
@@ -8,7 +8,7 @@
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', '-o', preferences_file, '--batch', igv_script], env=os.environ.copy())
+ exit_code = subprocess.call(['igv', '-g', 'genome.fa', '-o', preferences_file, '--batch', igv_script], env=os.environ.copy())
sys.exit(exit_code)