Mercurial > repos > jjohnson > gatk2
annotate tool_dependencies.xml @ 1:9b8e2a158073 draft
Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
author | Jim Johnson <jj@umn.edu> |
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date | Thu, 01 Nov 2012 13:44:41 -0500 |
parents | 74c05070a3f8 |
children | a65944bad5c1 |
rev | line source |
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0 | 1 <?xml version="1.0"?> |
2 <tool_dependency> | |
3 <package name="gatk" version="2.2"> | |
4 <install version="1.0"> | |
5 <actions> | |
6 <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-latest.tar.bz2</action> | |
1
9b8e2a158073
Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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7 <!-- this expands into GenomeAnalysisTKLite-2.2-2-gd3f5a5e/ |
9b8e2a158073
Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
8 which common_util.py tar_extraction_directory() does not find |
9b8e2a158073
Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
9 so the move file must contain the GenomeAnalysisTKLite-2.2-2-gd3f5a5e dir path |
9b8e2a158073
Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
10 --> |
0 | 11 <action type="move_file"> |
1
9b8e2a158073
Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
12 <source>GenomeAnalysisTKLite-2.2-2-gd3f5a5e/GenomeAnalysisTKLite.jar</source> |
0 | 13 <destination>$INSTALL_DIR/GenomeAnalysisTK.jar</destination> |
14 </action> | |
15 <action type="set_environment"> | |
16 <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable> | |
17 </action> | |
18 <action type="set_environment"> | |
19 <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD</environment_variable> | |
20 </action> | |
21 </actions> | |
22 </install> | |
23 <readme> | |
24 The following GATK2 analysis types require a License for commercial use and the full GATK2 build will need to be manually installed: | |
25 | |
26 haplotypecaller | |
27 HaplotypeCaller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an | |
28 active region. | |
29 HaplotypeResolver Haplotype-based resolution of variants in 2 different eval files. | |
30 | |
31 reducereads | |
32 CompareBAM Given two BAMs with different read groups, it compares them based on ReduceReads | |
33 metrics. | |
34 ReduceReads Reduces the BAM file using read based compression that keeps only essential information | |
35 for variant calling | |
36 | |
37 | |
38 See: http://www.appistry.com/gatk/gatk-faqs-static for Licensing details. | |
39 The full GATK build can be acquired from: http://www.broadinstitute.org/gatk/download | |
40 and GenomeAnalysisTK.jar need to be manually installed into the GATK2_PATH set for the GenomeAnalysisTKLite.jar | |
41 | |
42 The GATK2_SITE_OPTIONS environment variable can be modified in the env.sh in the tool_dependencies path can be modified | |
43 for the local installation. | |
44 | |
45 </readme> | |
46 </package> | |
47 <package name="samtools" version="0.1.18"> | |
48 <install version="1.0"> | |
49 <actions> | |
50 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> | |
51 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> | |
52 <action type="shell_command">make</action> | |
53 <action type="move_file"> | |
54 <source>samtools</source> | |
55 <destination>$INSTALL_DIR/bin</destination> | |
56 </action> | |
57 <action type="move_file"> | |
58 <source>misc/maq2sam-long</source> | |
59 <destination>$INSTALL_DIR/bin</destination> | |
60 </action> | |
61 <action type="set_environment"> | |
62 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
63 </action> | |
64 </actions> | |
65 </install> | |
66 <readme> | |
67 Compiling SAMtools requires the ncurses and zlib development libraries. | |
68 </readme> | |
69 </package> | |
70 </tool_dependency> |