Mercurial > repos > jjohnson > gatk2
annotate tool_dependencies.xml @ 17:f2b21dc45241 draft
Many fixes to haplotype_caller
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 15 Nov 2012 10:18:55 -0600 |
| parents | 35c6289faeff |
| children | 7533db8dfb5b |
| 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> | |
|
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35c6289faeff
Update tool_dependecies to GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2
Jim Johnson <jj@umn.edu>
parents:
9
diff
changeset
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6 <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2</action> |
| 0 | 7 <action type="move_file"> |
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15
35c6289faeff
Update tool_dependecies to GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2
Jim Johnson <jj@umn.edu>
parents:
9
diff
changeset
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8 <source>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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9 <destination>$INSTALL_DIR</destination> |
| 0 | 10 </action> |
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3
0edf813146d8
tool_dependencies.xml - fix move_file and add symlink
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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11 <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action> |
|
0edf813146d8
tool_dependencies.xml - fix move_file and add symlink
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
12 <action type="move_file"> |
|
0edf813146d8
tool_dependencies.xml - fix move_file and add symlink
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
13 <source>GenomeAnalysisTK.jar</source> |
|
0edf813146d8
tool_dependencies.xml - fix move_file and add symlink
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
14 <destination>$INSTALL_DIR</destination> |
|
0edf813146d8
tool_dependencies.xml - fix move_file and add symlink
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
15 </action> |
| 0 | 16 <action type="set_environment"> |
| 17 <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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18 <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 | 19 </action> |
| 20 </actions> | |
| 21 </install> | |
| 22 <readme> | |
| 23 The following GATK2 analysis types require a License for commercial use and the full GATK2 build will need to be manually installed: | |
| 24 | |
| 25 haplotypecaller | |
| 26 HaplotypeCaller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an | |
| 27 active region. | |
| 28 HaplotypeResolver Haplotype-based resolution of variants in 2 different eval files. | |
| 29 | |
| 30 reducereads | |
| 31 CompareBAM Given two BAMs with different read groups, it compares them based on ReduceReads | |
| 32 metrics. | |
| 33 ReduceReads Reduces the BAM file using read based compression that keeps only essential information | |
| 34 for variant calling | |
| 35 | |
| 36 | |
| 37 See: http://www.appistry.com/gatk/gatk-faqs-static for Licensing details. | |
| 38 The full GATK build can be acquired from: http://www.broadinstitute.org/gatk/download | |
| 39 and GenomeAnalysisTK.jar need to be manually installed into the GATK2_PATH set for the GenomeAnalysisTKLite.jar | |
| 40 | |
| 41 The GATK2_SITE_OPTIONS environment variable can be modified in the env.sh in the tool_dependencies path can be modified | |
| 42 for the local installation. | |
| 43 | |
| 44 </readme> | |
| 45 </package> | |
| 46 <package name="samtools" version="0.1.18"> | |
| 47 <install version="1.0"> | |
| 48 <actions> | |
| 49 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> | |
| 50 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> | |
| 51 <action type="shell_command">make</action> | |
| 52 <action type="move_file"> | |
| 53 <source>samtools</source> | |
| 54 <destination>$INSTALL_DIR/bin</destination> | |
| 55 </action> | |
| 56 <action type="move_file"> | |
| 57 <source>misc/maq2sam-long</source> | |
| 58 <destination>$INSTALL_DIR/bin</destination> | |
| 59 </action> | |
| 60 <action type="set_environment"> | |
| 61 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 62 </action> | |
| 63 </actions> | |
| 64 </install> | |
| 65 <readme> | |
| 66 Compiling SAMtools requires the ncurses and zlib development libraries. | |
| 67 </readme> | |
| 68 </package> | |
| 69 </tool_dependency> |