Mercurial > repos > iuc > package_samtools_0_1_19

comparison tool_dependencies.xml @ 8:0e56e4dac6e7 draft

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author iuc
date Thu, 26 Feb 2015 05:40:22 -0500
parents 8b98841b6b2f
children a0ab0fae27e5
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7:8b98841b6b2f 8:0e56e4dac6e7
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="c0735727b530" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="zlib" version="1.2.8">
7 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="samtools" version="0.1.19"> 3 <package name="samtools" version="0.1.19">
10 <install version="1.0"> 4 <install version="1.0">
11 <actions> 5 <actions_group>
12 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> 6 <actions os="linux" architecture="x86_64">
13 <action type="set_environment_for_install"> 7 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-Linux-x86_64.tgz</action>
14 <repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 8 <action type="move_directory_files">
15 <package name="ncurses" version="5.9" /> 9 <source_directory>.</source_directory>
16 </repository> 10 <destination_directory>$INSTALL_DIR</destination_directory>
17 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 11 </action>
18 <package name="zlib" version="1.2.8" /> 12 </actions>
19 </repository> 13 <actions os="darwin" architecture="x86_64">
14 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action>
15 <action type="move_directory_files">
16 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR</destination_directory>
18 </action>
19 </actions>
20 <actions>
21 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2</action>
22 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
23 <action type="shell_command">make</action>
24 <action type="move_file">
25 <source>samtools</source>
26 <destination>$INSTALL_DIR/bin</destination>
27 </action>
28 <action type="move_file">
29 <source>bcftools/bcftools</source>
30 <destination>$INSTALL_DIR/bin</destination>
31 </action>
32 <action type="move_file">
33 <source>bcftools/vcfutils.pl</source>
34 <destination>$INSTALL_DIR/bin</destination>
35 </action>
36 <action type="move_file">
37 <source>libbam.a</source>
38 <destination>$INSTALL_DIR/lib</destination>
39 </action>
40 <action type="move_directory_files">
41 <source_directory>.</source_directory>
42 <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
43 </action>
44 </actions>
45 <action type="set_environment">
46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
47 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
48 <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
20 </action> 49 </action>
21 <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action> 50 </actions_group>
22 <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action>
23 <action type="shell_command">make</action>
24 <action type="move_file">
25 <source>samtools</source>
26 <destination>$INSTALL_DIR/bin</destination>
27 </action>
28 <action type="set_environment">
29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
30 </action>
31 </actions>
32 </install> 51 </install>
33 <readme> 52 <readme>
34 Program: samtools (Tools for alignments in the SAM format) 53 Program: samtools (Tools for alignments in the SAM format)
35 Version: 0.1.19 54 Version: 0.1.19-44428cd
36 55
37 Usage: samtools &lt;command&gt; [options] 56 Usage: samtools &lt;command&gt; [options]
38 57
39 Command: view SAM&lt;-&gt;BAM conversion 58 Command: view SAM&lt;-&gt;BAM conversion
40 sort sort alignment file 59 sort sort alignment file
49 calmd recalculate MD/NM tags and '=' bases 68 calmd recalculate MD/NM tags and '=' bases
50 merge merge sorted alignments 69 merge merge sorted alignments
51 rmdup remove PCR duplicates 70 rmdup remove PCR duplicates
52 reheader replace BAM header 71 reheader replace BAM header
53 cat concatenate BAMs 72 cat concatenate BAMs
73 bedcov read depth per BED region
54 targetcut cut fosmid regions (for fosmid pool only) 74 targetcut cut fosmid regions (for fosmid pool only)
55 phase phase heterozygotes 75 phase phase heterozygotes
56 76 bamshuf shuffle and group alignments by name
57 Requirements: libncurses header files
58 </readme> 77 </readme>
59 </package> 78 </package>
60 </tool_dependency> 79 </tool_dependency>