Mercurial > repos > jjohnson > package_rsem_1_1_17
annotate tool_dependencies.xml @ 1:7d060ea51c6f default tip
RSEM needs samtools in relative path to install
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 05 Dec 2013 08:39:51 -0600 |
| parents | 9fa1826ae6d4 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="rsem" version="1.1.17"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.1.17.tar.gz</action> | |
| 7 <action type="shell_command">make</action> | |
|
1
7d060ea51c6f
RSEM needs samtools in relative path to install
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
8 <action type="make_directory">$INSTALL_DIR/bin/sam</action> |
|
7d060ea51c6f
RSEM needs samtools in relative path to install
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
9 <action type="move_file"> |
|
7d060ea51c6f
RSEM needs samtools in relative path to install
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
10 <source>sam/samtools</source> |
|
7d060ea51c6f
RSEM needs samtools in relative path to install
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
11 <destination>$INSTALL_DIR/bin/sam</destination> |
|
7d060ea51c6f
RSEM needs samtools in relative path to install
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
12 </action> |
| 0 | 13 <action type="move_file"> |
| 14 <source>convert-sam-for-rsem</source> | |
| 15 <destination>$INSTALL_DIR/bin</destination> | |
| 16 </action> | |
| 17 <action type="move_file"> | |
| 18 <source>extract-transcript-to-gene-map-from-trinity</source> | |
| 19 <destination>$INSTALL_DIR/bin</destination> | |
| 20 </action> | |
| 21 <action type="move_file"> | |
| 22 <source>rsem-bam2readdepth</source> | |
| 23 <destination>$INSTALL_DIR/bin</destination> | |
| 24 </action> | |
| 25 <action type="move_file"> | |
| 26 <source>rsem-bam2wig</source> | |
| 27 <destination>$INSTALL_DIR/bin</destination> | |
| 28 </action> | |
| 29 <action type="move_file"> | |
| 30 <source>rsem-build-read-index</source> | |
| 31 <destination>$INSTALL_DIR/bin</destination> | |
| 32 </action> | |
| 33 <action type="move_file"> | |
| 34 <source>rsem-calculate-credibility-intervals</source> | |
| 35 <destination>$INSTALL_DIR/bin</destination> | |
| 36 </action> | |
| 37 <action type="move_file"> | |
| 38 <source>rsem-calculate-expression</source> | |
| 39 <destination>$INSTALL_DIR/bin</destination> | |
| 40 </action> | |
| 41 <action type="move_file"> | |
| 42 <source>rsem-extract-reference-transcripts</source> | |
| 43 <destination>$INSTALL_DIR/bin</destination> | |
| 44 </action> | |
| 45 <action type="move_file"> | |
| 46 <source>rsem-gen-transcript-plots</source> | |
| 47 <destination>$INSTALL_DIR/bin</destination> | |
| 48 </action> | |
| 49 <action type="move_file"> | |
| 50 <source>rsem-get-unique</source> | |
| 51 <destination>$INSTALL_DIR/bin</destination> | |
| 52 </action> | |
| 53 <action type="move_file"> | |
| 54 <source>rsem-parse-alignments</source> | |
| 55 <destination>$INSTALL_DIR/bin</destination> | |
| 56 </action> | |
| 57 <action type="move_file"> | |
| 58 <source>rsem-plot-model</source> | |
| 59 <destination>$INSTALL_DIR/bin</destination> | |
| 60 </action> | |
| 61 <action type="move_file"> | |
| 62 <source>rsem-plot-transcript-wiggles</source> | |
| 63 <destination>$INSTALL_DIR/bin</destination> | |
| 64 </action> | |
| 65 <action type="move_file"> | |
| 66 <source>rsem-prepare-reference</source> | |
| 67 <destination>$INSTALL_DIR/bin</destination> | |
| 68 </action> | |
| 69 <action type="move_file"> | |
| 70 <source>rsem-preref</source> | |
| 71 <destination>$INSTALL_DIR/bin</destination> | |
| 72 </action> | |
| 73 <action type="move_file"> | |
| 74 <source>rsem-run-em</source> | |
| 75 <destination>$INSTALL_DIR/bin</destination> | |
| 76 </action> | |
| 77 <action type="move_file"> | |
| 78 <source>rsem-run-gibbs</source> | |
| 79 <destination>$INSTALL_DIR/bin</destination> | |
| 80 </action> | |
| 81 <action type="move_file"> | |
| 82 <source>rsem-simulate-reads</source> | |
| 83 <destination>$INSTALL_DIR/bin</destination> | |
| 84 </action> | |
| 85 <action type="move_file"> | |
| 86 <source>rsem-synthesis-reference-transcripts</source> | |
| 87 <destination>$INSTALL_DIR/bin</destination> | |
| 88 </action> | |
| 89 <action type="move_file"> | |
| 90 <source>rsem-tbam2gbam</source> | |
| 91 <destination>$INSTALL_DIR/bin</destination> | |
| 92 </action> | |
| 93 <action type="set_environment"> | |
| 94 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 95 </action> | |
| 96 </actions> | |
| 97 </install> | |
| 98 <readme> | |
| 99 RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly | |
| 100 interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, | |
| 101 variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95X credibility interval estimates for expression levels. | |
| 102 For visualization,It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files | |
| 103 can be visualized by both UCSC Genome browser and Broad InstituteXs Integrative Genomics Viewer (IGV). | |
| 104 Transcript-coordinate files can be visualized by IGV. | |
| 105 | |
| 106 http://deweylab.biostat.wisc.edu/rsem/README.html | |
| 107 http://deweylab.biostat.wisc.edu/rsem/ | |
| 108 </readme> | |
| 109 </package> | |
| 110 </tool_dependency> |