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7d3d7eb @chapmanb YAML configuration file for custom installs
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1 ---
2 # List of custom programs to install that are not packaged. These each require
3 # a install_name function in the appropriate place in the 'custom' directory to
4 # define the steps for downloading, building, and installing the package.
5dcedb0 @chapmanb emboss and macs install targets; update custom next-get libraries for…
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5 bio_general:
6 - emboss
1245fee @chapmanb Generate genome data; generalize software installs into main Biolinux…
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7 bio_nextgen:
06a2418 @chapmanb Finalize intall on virtualbox/vagrant; include additional next gen so…
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8 alignment:
298b0c2 @chapmanb Small fixes for automation on 64 bit builds
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9 - bwa
10 - bowtie
cdfa26d @chapmanb Add additional packages: tophat, cufflinks, gmap, bedtools, freebayes…
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11 - gmap
8b3605f @chapmanb Lastz alignment
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12 - lastz
8040470 @chapmanb mosaik aligner custom install instructions; thanks to Amit Indap for …
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13 - mosaik
06a2418 @chapmanb Finalize intall on virtualbox/vagrant; include additional next gen so…
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14 - perm
d0d0cf6 @chapmanb Build target for sabre; barcode de-mulitplexing
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15 utilitites:
cdfa26d @chapmanb Add additional packages: tophat, cufflinks, gmap, bedtools, freebayes…
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16 - bedtools
6c91004 @chapmanb Add fastqc to custom packages; avoid re-setting user in fabricrc. Now…
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17 - fastqc
298b0c2 @chapmanb Small fixes for automation on 64 bit builds
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18 - fastx_toolkit
d0d0cf6 @chapmanb Build target for sabre; barcode de-mulitplexing
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19 - sabre
20 - solexaqa
21 analysis:
22 - cufflinks
cdfa26d @chapmanb Add additional packages: tophat, cufflinks, gmap, bedtools, freebayes…
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23 - freebayes
6530436 @chapmanb Data retrieval: get additional liftOver versions and BLAST indexed un…
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24 - gatk
25 - picard
4bfb002 @chapmanb Install target for shrec k-mer read filtration
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26 - shrec
2c73ab4 @chapmanb Add snpeff build instructions
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27 - snpeff
1dff356 @chapmanb Hook for individual installation of custom packages; add solexqa install
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28 - tophat
06a2418 @chapmanb Finalize intall on virtualbox/vagrant; include additional next gen so…
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29 assembly:
30 - abyss
f9efd00 @chapmanb Additional generalization for RPM systems; provide new build targets …
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31 - transabyss
32 - trinity
06a2418 @chapmanb Finalize intall on virtualbox/vagrant; include additional next gen so…
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33 - velvet
5dcedb0 @chapmanb emboss and macs install targets; update custom next-get libraries for…
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34 chip:
35 - macs
82e926f @chapmanb Roll in additional libraries and suggestions from Codefest: Perl modu…
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36 needs_64bit:
37 - ucsc_tools
38 - bfast
d44bd62 @chapmanb Add novoalign to image; provide indexed genomes in data snapshot
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39 - novoalign
06a2418 @chapmanb Finalize intall on virtualbox/vagrant; include additional next gen so…
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40 distributed:
41 - mahout
42 - pydoop
a064cb1 @chapmanb Custom python libraries with problems from easy_install
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43 python:
44 - bx-python
45 - matplotlib
46 - rpy
06a2418 @chapmanb Finalize intall on virtualbox/vagrant; include additional next gen so…
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47 java:
48 - leinengin
f975da3 @chapmanb Improve documentation for rolling out EC2 images
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49 #- cljr
cdfa26d @chapmanb Add additional packages: tophat, cufflinks, gmap, bedtools, freebayes…
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50 # ToDo -- test on 64bit with bfast
51 #- dnaa
52 #- srma
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