Mercurial > repos > devteam > package_samtools_0_1_16

comparison tool_dependencies.xml @ 1:3cc494fb5a14 draft default tip

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Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
author devteam
date Wed, 25 Sep 2013 10:50:18 -0400
parents 75367f13eb3c
children
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0:75367f13eb3c 1:3cc494fb5a14
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="samtools" version="0.1.16"> 3 <package name="samtools" version="0.1.16">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions_group>
6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.16/samtools-0.1.16.tar.bz2</action> 6 <actions os="linux" architecture="i386">
7 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> 7 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action>
8 <action type="shell_command">make</action> 8 <action type="move_directory_files">
9 <action type="move_file"> 9 <source_directory>.</source_directory>
10 <source>samtools</source> 10 <destination_directory>$INSTALL_DIR</destination_directory>
11 <destination>$INSTALL_DIR/bin</destination> 11 </action>
12 </action> 12 </actions>
13 <actions os="linux" architecture="x86_64">
14 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action>
15 <action type="move_directory_files">
16 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR</destination_directory>
18 </action>
19 </actions>
20 <actions os="darwin" architecture="i386">
21 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action>
22 <action type="move_directory_files">
23 <source_directory>.</source_directory>
24 <destination_directory>$INSTALL_DIR</destination_directory>
25 </action>
26 </actions>
27 <actions os="darwin" architecture="x86_64">
28 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action>
29 <action type="move_directory_files">
30 <source_directory>.</source_directory>
31 <destination_directory>$INSTALL_DIR</destination_directory>
32 </action>
33 </actions>
34 <actions>
35 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action>
36 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
37 <action type="shell_command">make</action>
38 <action type="move_file">
39 <source>samtools</source>
40 <destination>$INSTALL_DIR/bin</destination>
41 </action>
42 <action type="move_file">
43 <source>libbam.a</source>
44 <destination>$INSTALL_DIR/lib</destination>
45 </action>
46 </actions>
13 <action type="set_environment"> 47 <action type="set_environment">
14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 48 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
49 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
15 </action> 50 </action>
16 </actions> 51 </actions_group>
17 </install> 52 </install>
18 <readme> 53 <readme>
19 This is the last version of SAMTools to include the 'pileup' command. 54 This is the last version of SAMTools to include the 'pileup' command.
20 55
21 Program: samtools (Tools for alignments in the SAM format) 56 Program: samtools (Tools for alignments in the SAM format)