Mercurial > repos > iuc > package_samtools_0_1_19

comparison tool_dependencies.xml @ 2:b471600c8a3b draft

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author bgruening
date Sun, 27 Apr 2014 14:28:10 -0400
parents 00e17a794a2e
children 6b6b5498d9a2
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1:00e17a794a2e 2:b471600c8a3b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="ncurses" version="5.9">
4 <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package>
3 <package name="samtools" version="0.1.19"> 6 <package name="samtools" version="0.1.19">
4 <install version="1.0"> 7 <install version="1.0">
5 <actions> 8 <actions>
6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> 9 <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> 10 <action type="set_environment_for_install">
11 <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
12 <package name="ncurses" version="5.9" />
13 </repository>
14 </action>
15 <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action>
16 <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -L$NCURSES_LIB_PATH|g" Makefile</action>
8 <action type="shell_command">make</action> 17 <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>
12 <action type="move_file"> 18 <action type="move_file">
13 <source>samtools</source> 19 <source>samtools</source>
14 <destination>$INSTALL_DIR/bin</destination> 20 <destination>$INSTALL_DIR/bin</destination>
15 </action> 21 </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>$INSTALL_DIR/bin</destination_directory>
27 </action>
28 <action type="set_environment"> 22 <action type="set_environment">
29 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
30 </action> 24 </action>
31 </actions> 25 </actions>
32 </install> 26 </install>
33 <readme> 27 <readme>
34 Program: samtools (Tools for alignments in the SAM format) 28 Program: samtools (Tools for alignments in the SAM format)
52 reheader replace BAM header 46 reheader replace BAM header
53 cat concatenate BAMs 47 cat concatenate BAMs
54 targetcut cut fosmid regions (for fosmid pool only) 48 targetcut cut fosmid regions (for fosmid pool only)
55 phase phase heterozygotes 49 phase phase heterozygotes
56 50
57 This also installs bcftools and misc utility commands: 51 Requirements: libncurses header files
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
79 </readme> 52 </readme>
80 </package> 53 </package>
81 </tool_dependency> 54 </tool_dependency>