Mercurial > repos > jjohnson > gatk2
annotate tool_dependencies.xml @ 9:24504f5cac5e draft
Fix dir path to GenomeAnalysisTKLite.jar
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 06 Nov 2012 11:48:49 -0600 |
| parents | e5eac3c0ce10 |
| children | 35c6289faeff |
| rev | line source |
|---|---|
| 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> | |
| 8 | 7 <!-- this expands into GenomeAnalysisTKLite-2.2-3-g63dddfb/ |
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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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8 which common_util.py tar_extraction_directory() does not find |
| 8 | 9 so the move file must contain the GenomeAnalysisTKLite-2.2-3-g63dddfb dir path |
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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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10 --> |
| 0 | 11 <action type="move_file"> |
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9
24504f5cac5e
Fix dir path to GenomeAnalysisTKLite.jar
Jim Johnson <jj@umn.edu>
parents:
8
diff
changeset
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12 <source>GenomeAnalysisTKLite-2.2-3-g63dddfb/GenomeAnalysisTKLite.jar</source> |
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2
a65944bad5c1
tool_dependencies.xml - fix move_file and add symlink
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
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13 <destination>$INSTALL_DIR</destination> |
| 0 | 14 </action> |
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3
0edf813146d8
tool_dependencies.xml - fix move_file and add symlink
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
15 <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action> |
|
0edf813146d8
tool_dependencies.xml - fix move_file and add symlink
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
16 <action type="move_file"> |
|
0edf813146d8
tool_dependencies.xml - fix move_file and add symlink
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
17 <source>GenomeAnalysisTK.jar</source> |
|
0edf813146d8
tool_dependencies.xml - fix move_file and add symlink
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
18 <destination>$INSTALL_DIR</destination> |
|
0edf813146d8
tool_dependencies.xml - fix move_file and add symlink
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
19 </action> |
| 0 | 20 <action type="set_environment"> |
| 21 <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable> | |
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5
0ed800373b59
Quote the tool_dependencies.xml GATK2_SITE_OPTIONS action text
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
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22 <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">"--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD"</environment_variable> |
| 0 | 23 </action> |
| 24 </actions> | |
| 25 </install> | |
| 26 <readme> | |
| 27 The following GATK2 analysis types require a License for commercial use and the full GATK2 build will need to be manually installed: | |
| 28 | |
| 29 haplotypecaller | |
| 30 HaplotypeCaller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an | |
| 31 active region. | |
| 32 HaplotypeResolver Haplotype-based resolution of variants in 2 different eval files. | |
| 33 | |
| 34 reducereads | |
| 35 CompareBAM Given two BAMs with different read groups, it compares them based on ReduceReads | |
| 36 metrics. | |
| 37 ReduceReads Reduces the BAM file using read based compression that keeps only essential information | |
| 38 for variant calling | |
| 39 | |
| 40 | |
| 41 See: http://www.appistry.com/gatk/gatk-faqs-static for Licensing details. | |
| 42 The full GATK build can be acquired from: http://www.broadinstitute.org/gatk/download | |
| 43 and GenomeAnalysisTK.jar need to be manually installed into the GATK2_PATH set for the GenomeAnalysisTKLite.jar | |
| 44 | |
| 45 The GATK2_SITE_OPTIONS environment variable can be modified in the env.sh in the tool_dependencies path can be modified | |
| 46 for the local installation. | |
| 47 | |
| 48 </readme> | |
| 49 </package> | |
| 50 <package name="samtools" version="0.1.18"> | |
| 51 <install version="1.0"> | |
| 52 <actions> | |
| 53 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> | |
| 54 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> | |
| 55 <action type="shell_command">make</action> | |
| 56 <action type="move_file"> | |
| 57 <source>samtools</source> | |
| 58 <destination>$INSTALL_DIR/bin</destination> | |
| 59 </action> | |
| 60 <action type="move_file"> | |
| 61 <source>misc/maq2sam-long</source> | |
| 62 <destination>$INSTALL_DIR/bin</destination> | |
| 63 </action> | |
| 64 <action type="set_environment"> | |
| 65 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 66 </action> | |
| 67 </actions> | |
| 68 </install> | |
| 69 <readme> | |
| 70 Compiling SAMtools requires the ncurses and zlib development libraries. | |
| 71 </readme> | |
| 72 </package> | |
| 73 </tool_dependency> |