Mercurial > repos > mvdbeek > igv_take_screenshots

annotate xvfb_igv.py @ 16:817db6799e96 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1ddb87e95baeea2a4ee9b95930da6e0927fb7ff7-dirty
author mvdbeek
date Fri, 28 Jul 2017 12:56:38 -0400
parents 1100d5a77c4d
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d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
diff changeset
1 import os
d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
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2 import subprocess
d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
diff changeset
3 import sys
d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
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d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
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5 import xvfbwrapper
d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
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d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
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64eb1ffd7872 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents: 0
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8 def take_screenshots(igv_script, preferences_file, screensize):
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d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
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9 width, height = screensize.split(',')
d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
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10 with xvfbwrapper.Xvfb(width=width, height=height) as xvfb:
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1100d5a77c4d planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1ddb87e95baeea2a4ee9b95930da6e0927fb7ff7-dirty
mvdbeek
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11 exit_code = subprocess.call(['igv', '-g', 'genome.fa', '-o', preferences_file, '--batch', igv_script], env=os.environ.copy())
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d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
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12 sys.exit(exit_code)
d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
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d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
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d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
parents:
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15 if __name__ == '__main__':
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64eb1ffd7872 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
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16 take_screenshots(sys.argv[1], sys.argv[2], sys.argv[3])
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d828cf6bff42 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4824aeaa8107bd30ec786e8ca81779f053f0e736-dirty
mvdbeek
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