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