Mercurial > repos > iuc > package_samtools_0_1_19
annotate tool_dependencies.xml @ 4:279806044d60 draft
Uploaded
author | iuc |
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date | Mon, 21 Jul 2014 09:03:03 -0400 |
parents | 6b6b5498d9a2 |
children | 923adc89c666 |
rev | line source |
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0 | 1 <?xml version="1.0"?> |
2 <tool_dependency> | |
2 | 3 <package name="ncurses" version="5.9"> |
3 | 4 <repository changeset_revision="71e3f4bfd1a9" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> |
2 | 5 </package> |
4 | 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> | |
0 | 9 <package name="samtools" version="0.1.19"> |
10 <install version="1.0"> | |
11 <actions> | |
12 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> | |
2 | 13 <action type="set_environment_for_install"> |
3 | 14 <repository changeset_revision="71e3f4bfd1a9" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> |
2 | 15 <package name="ncurses" version="5.9" /> |
16 </repository> | |
17 </action> | |
18 <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action> | |
3 | 19 <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$NCURSES_LIB_PATH|g" Makefile</action> |
0 | 20 <action type="shell_command">make</action> |
21 <action type="move_file"> | |
22 <source>samtools</source> | |
23 <destination>$INSTALL_DIR/bin</destination> | |
24 </action> | |
25 <action type="set_environment"> | |
2 | 26 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
0 | 27 </action> |
28 </actions> | |
29 </install> | |
30 <readme> | |
31 Program: samtools (Tools for alignments in the SAM format) | |
32 Version: 0.1.19 | |
33 | |
34 Usage: samtools <command> [options] | |
35 | |
36 Command: view SAM<->BAM conversion | |
37 sort sort alignment file | |
38 mpileup multi-way pileup | |
39 depth compute the depth | |
40 faidx index/extract FASTA | |
41 tview text alignment viewer | |
42 index index alignment | |
43 idxstats BAM index stats (r595 or later) | |
44 fixmate fix mate information | |
45 flagstat simple stats | |
46 calmd recalculate MD/NM tags and '=' bases | |
47 merge merge sorted alignments | |
48 rmdup remove PCR duplicates | |
49 reheader replace BAM header | |
50 cat concatenate BAMs | |
51 targetcut cut fosmid regions (for fosmid pool only) | |
52 phase phase heterozygotes | |
1
00e17a794a2e
Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents:
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53 |
2 | 54 Requirements: libncurses header files |
0 | 55 </readme> |
56 </package> | |
57 </tool_dependency> |