Mercurial > repos > iuc > package_samtools_0_1_19

annotate tool_dependencies.xml @ 1:00e17a794a2e

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Also install bcftools and misc utility commands when installing samtools.
author Jim Johnson <jj@umn.edu>
date Tue, 17 Sep 2013 11:36:59 -0500
parents cb87eae7fc3e
children b471600c8a3b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
2 <tool_dependency>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
3 <package name="samtools" version="0.1.19">
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
4 <install version="1.0">
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
5 <actions>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
7 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
8 <action type="shell_command">make</action>
1
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
9 <action type="shell_command">chmod ugo+rx misc/*.p?</action>
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
10 <action type="shell_command">mkdir misc/bin</action>
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
11 <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</action>
0
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
12 <action type="move_file">
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
13 <source>samtools</source>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
14 <destination>$INSTALL_DIR/bin</destination>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
15 </action>
1
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
16 <action type="move_file">
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
17 <source>bcftools/bcftools</source>
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
18 <destination>$INSTALL_DIR/bin</destination>
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
19 </action>
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
20 <action type="move_file">
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
21 <source>bcftools/vcfutils.pl</source>
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
22 <destination>$INSTALL_DIR/bin</destination>
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
23 </action>
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
24 <action type="move_directory_files">
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
25 <source_directory>misc/bin</source_directory>
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
26 <destination_directory>$INSTALL_DIR/bin</destination_directory>
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
27 </action>
0
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
28 <action type="set_environment">
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
29 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
30 </action>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
31 </actions>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
32 </install>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
33 <readme>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
34 Program: samtools (Tools for alignments in the SAM format)
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
35 Version: 0.1.19
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
36
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
37 Usage: samtools &lt;command&gt; [options]
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
38
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
39 Command: view SAM&lt;-&gt;BAM conversion
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
40 sort sort alignment file
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
41 mpileup multi-way pileup
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
42 depth compute the depth
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
43 faidx index/extract FASTA
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
44 tview text alignment viewer
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
45 index index alignment
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
46 idxstats BAM index stats (r595 or later)
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
47 fixmate fix mate information
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
48 flagstat simple stats
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
49 calmd recalculate MD/NM tags and '=' bases
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
50 merge merge sorted alignments
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
51 rmdup remove PCR duplicates
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
52 reheader replace BAM header
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
53 cat concatenate BAMs
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
54 targetcut cut fosmid regions (for fosmid pool only)
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
55 phase phase heterozygotes
1
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
56
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
57 This also installs bcftools and misc utility commands:
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
58 bcftools
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
59 vcfutils.pl
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
60 ace2sam
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
61 bamcheck
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
62 blast2sam.pl
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
63 bowtie2sam.pl
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
64 export2sam.pl
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
65 interpolate_sam.pl
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
66 maq2sam-long
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
67 maq2sam-short
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
68 md5fa
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
69 md5sum-lite
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
70 novo2sam.pl
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
71 psl2sam.pl
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
72 sam2vcf.pl
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
73 samtools.pl
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
74 soap2sam.pl
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
75 varfilter.py
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
76 wgsim
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
77 wgsim_eval.pl
00e17a794a2e Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
78 zoom2sam.pl
0
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
79 </readme>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
80 </package>
cb87eae7fc3e Uploaded
iuc
parents:
diff changeset
81 </tool_dependency>