Mercurial > repos > matces > carpet_toolsuite
comparison carpet-src-1/INSTALL @ 0:cdd489d98766
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | matces |
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| date | Tue, 07 Jun 2011 16:50:41 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:cdd489d98766 |
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| 1 Prerequisites: | |
| 2 - a working installation of galaxy | |
| 3 - R/Bioconductor | |
| 4 - Ringo bioconductor library | |
| 5 - rpy (version 1.0.x) | |
| 6 - a working C++ compiler | |
| 7 | |
| 8 Installation: | |
| 9 given a galaxy dir $GALAXYTOPDIR | |
| 10 - extract the content of the archive into $GALAXYTOPDIR: | |
| 11 | |
| 12 tar cvjf carpet.tar.bz2 -C $GALAXYTOPDIR | |
| 13 | |
| 14 - build the "comuni" executable: | |
| 15 | |
| 16 cd $GALAXYTOPDIR/tools/CARPET | |
| 17 g++ com_uni.cpp -o comuni | |
| 18 | |
| 19 (do NOT use optimizations if possible) | |
| 20 | |
| 21 - paste the content of add_to_tool_conf.xml within tool_conf.xml | |
| 22 file (part of galaxy distribution), where needed and between the | |
| 23 <toolbox></toolbox> tags | |
| 24 | |
| 25 - restart galaxy | |
| 26 | |
| 27 NOTES: | |
| 28 - rpy2 is not implemented in carpet yet. You can download rpy (1.0.3) here: | |
| 29 | |
| 30 http://sourceforge.net/projects/rpy/files/rpy/1.0.3/rpy-1.0.3.tar.gz/download | |
| 31 | |
| 32 - You may install bioconductor's Ringo library just issuing the following within | |
| 33 your R console: | |
| 34 | |
| 35 source("http://bioconductor.org/biocLite.R") | |
| 36 biocLite("Ringo") | |
| 37 | |
| 38 - carpet has been deployed and tested on galaxy build 1349. There's no warranty it | |
| 39 works on different builds (although it should). |