Mercurial > repos > iuc > package_samtools_0_1_19

comparison tool_dependencies.xml @ 1:54195f1d4b0f

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Also install bcftools and misc utility commands when installing samtools.
author Jim Johnson <jj@umn.edu>
date Tue, 17 Sep 2013 11:31:38 -0500
parents 18ccfc4b9542
children 9f412e12b103
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0:18ccfc4b9542 1:54195f1d4b0f
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions>
6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> 6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
7 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> 7 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
8 <action type="shell_command">make</action> 8 <action type="shell_command">make</action>
9 <action type="shell_command">chmod ugo+rx misc/*.p?</action>
10 <action type="shell_command">mkdir misc/bin</action>
11 <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</action>
9 <action type="move_file"> 12 <action type="move_file">
10 <source>samtools</source> 13 <source>samtools</source>
11 <destination>$INSTALL_DIR/bin</destination> 14 <destination>$INSTALL_DIR/bin</destination>
15 </action>
16 <action type="move_file">
17 <source>bcftools/bcftools</source>
18 <destination>$INSTALL_DIR/bin</destination>
19 </action>
20 <action type="move_file">
21 <source>bcftools/vcfutils.pl</source>
22 <destination>$INSTALL_DIR/bin</destination>
23 </action>
24 <action type="move_directory_files">
25 <source_directory>misc/bin</source_directory>
26 <destination_directory>$INSTALL_DIR/bin</destination_directory>
12 </action> 27 </action>
13 <action type="set_environment"> 28 <action type="set_environment">
14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 29 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
15 </action> 30 </action>
16 </actions> 31 </actions>
36 rmdup remove PCR duplicates 51 rmdup remove PCR duplicates
37 reheader replace BAM header 52 reheader replace BAM header
38 cat concatenate BAMs 53 cat concatenate BAMs
39 targetcut cut fosmid regions (for fosmid pool only) 54 targetcut cut fosmid regions (for fosmid pool only)
40 phase phase heterozygotes 55 phase phase heterozygotes
56
57 This also installs bcftools and misc utility commands:
58 bcftools
59 vcfutils.pl
60 ace2sam
61 bamcheck
62 blast2sam.pl
63 bowtie2sam.pl
64 export2sam.pl
65 interpolate_sam.pl
66 maq2sam-long
67 maq2sam-short
68 md5fa
69 md5sum-lite
70 novo2sam.pl
71 psl2sam.pl
72 sam2vcf.pl
73 samtools.pl
74 soap2sam.pl
75 varfilter.py
76 wgsim
77 wgsim_eval.pl
78 zoom2sam.pl
41 </readme> 79 </readme>
42 </package> 80 </package>
43 </tool_dependency> 81 </tool_dependency>