Mercurial > repos > iuc > package_samtools_0_1_19
comparison tool_dependencies.xml @ 6:96aab723499f draft
Uploaded
author | iuc |
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date | Thu, 26 Feb 2015 14:21:15 -0500 |
parents | 923adc89c666 |
children | c9bd782f5342 |
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5:923adc89c666 | 6:96aab723499f |
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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="71e3f4bfd1a9" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> | |
5 </package> | |
6 <package name="zlib" version="1.2.8"> | |
7 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.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="71e3f4bfd1a9" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.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>$INSTALL_DIR</destination_directory> |
17 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> | 11 </action> |
18 <package name="zlib" version="1.2.8" /> | 12 </actions> |
19 </repository> | 13 <actions os="darwin" architecture="x86_64"> |
14 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action> | |
15 <action type="move_directory_files"> | |
16 <source_directory>.</source_directory> | |
17 <destination_directory>$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 '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 <command> [options] | 56 Usage: samtools <command> [options] |
38 | 57 |
39 Command: view SAM<->BAM conversion | 58 Command: view SAM<->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> |