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jlec 13/12/29 00:24:16 |
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Added: amos-3.1.0-goBambus2.py-indent-and-cleanup.patch |
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Log: |
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sci-biology/amos: Fix python support |
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(Portage version: 2.2.7/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
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Revision Changes Path |
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1.1 sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch |
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch?rev=1.1&content-type=text/plain |
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Index: amos-3.1.0-goBambus2.py-indent-and-cleanup.patch |
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=================================================================== |
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--- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 |
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+++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 |
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@@ -1,7 +1,7 @@ |
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#pipeline script for assembly + Bambus 2 |
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#contributed by Todd J Treangen |
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-import string, sys, os, subprocess#, spincursor |
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+import sys, os, subprocess#, spincursor |
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RED = "\033[0;31m" |
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GREEN = "\033[0;32m" |
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@@ -360,7 +360,7 @@ |
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print "\t\t%s...failed%s"%(RED,NONE) |
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sys.exit(1) |
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- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) |
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+ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) |
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if xopt_dict["verbose"] == 1: |
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print "10) running OutputResults" |
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@@ -388,4 +388,3 @@ |
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else: |
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print "\t\t%s...failed%s"%(RED,NONE) |
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sys.exit(1) |
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-) |
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