https://github.com/genome/genome
- HEAD
- refs/for/master
- refs/heads/chrisamiller-patch-1
- refs/heads/cle
- refs/heads/cle-snapshot
- refs/heads/cle-staging
- refs/heads/cram
- refs/heads/cwltool-path
- refs/heads/gms-pub
- refs/heads/gms-pub-2015.02.22
- refs/heads/gms-pub-2015.03.04
- refs/heads/gms-pub-before-plos-merge-from-master
- refs/heads/gotcloud
- refs/heads/master
- refs/heads/mcallawa_trusty
- refs/heads/model-tests
- refs/heads/model-tests-for-lsf9
- refs/heads/perl-tests
- refs/heads/revert-606-gmt_picard_typos
- refs/heads/snapshot
- refs/tags/AP-103
- refs/tags/genome-3177
- refs/tags/genome-3178
- refs/tags/genome-3179
- refs/tags/genome-3180
- refs/tags/genome-3181
- refs/tags/genome-3182
- refs/tags/genome-3183
- refs/tags/genome-3184
- refs/tags/genome-3185
- refs/tags/genome-3186
- refs/tags/genome-3187
- refs/tags/genome-3188
- refs/tags/genome-3189
- refs/tags/genome-3190
- refs/tags/genome-3191
- refs/tags/genome-3192
- refs/tags/genome-3194
- refs/tags/genome-3196
- refs/tags/genome-3197
- refs/tags/genome-3198
- refs/tags/genome-3199
- refs/tags/genome-3200
- refs/tags/genome-3201
- refs/tags/genome-3202
- refs/tags/genome-3203
- refs/tags/genome-3204
- refs/tags/genome-3206
- refs/tags/genome-3207
- refs/tags/genome-3209
- refs/tags/genome-3210
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- refs/tags/genome-3250
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- refs/tags/genome-3257
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- refs/tags/genome-3259
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- refs/tags/genome-3274
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- refs/tags/genome-3278
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- refs/tags/genome-3289
- refs/tags/genome-3292
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- refs/tags/genome-3310
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- refs/tags/genome-3321
- refs/tags/genome-3322
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- refs/tags/genome-3324
- refs/tags/genome-3325
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- refs/tags/genome-3327
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- refs/tags/genome-3333
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- refs/tags/genome-3376
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- refs/tags/genome-3378
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- refs/tags/genome-3380
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- refs/tags/genome-3383
- refs/tags/genome-3384
- refs/tags/genome-3385
- refs/tags/genome-3386
- refs/tags/genome-3387
- refs/tags/genome-3388
- refs/tags/genome-3389
- refs/tags/genome-3390
- refs/tags/genome-3391
- refs/tags/genome-3392
- refs/tags/genome-3393
- refs/tags/genome-3394
- refs/tags/genome-3395
- refs/tags/genome-3396
- refs/tags/genome-3397
- refs/tags/genome-3398
- refs/tags/genome-3399
- refs/tags/genome-3400
- refs/tags/genome-3401
- refs/tags/genome-3402
- refs/tags/genome-3403
- refs/tags/genome-3404
- refs/tags/genome-3405
- refs/tags/genome-3406
- refs/tags/genome-3407
- refs/tags/genome-3408
- refs/tags/genome-3409
- refs/tags/genome-3410
- refs/tags/genome-3411
- refs/tags/genome-3412
- refs/tags/genome-3413
- refs/tags/genome-3414
- refs/tags/genome-3415
- refs/tags/genome-3416
- refs/tags/genome-3417
- refs/tags/genome-3418
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- refs/tags/genome-3420
- refs/tags/genome-3421
- refs/tags/genome-3422
- refs/tags/genome-3423
- refs/tags/genome-3424
- refs/tags/genome-3425
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- refs/tags/genome-3430
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- refs/tags/genome-3465
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- refs/tags/genome-3521
- refs/tags/genome-3522
- refs/tags/genome-3523
- refs/tags/genome-3524
- refs/tags/genome-3525
- refs/tags/genome-3526
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- refs/tags/genome-3528
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- refs/tags/genome-3659
- refs/tags/genome-3660
- refs/tags/genome-3661
- refs/tags/genome-3662
- refs/tags/genome-3663
- refs/tags/genome-3664
- refs/tags/genome-3665
- refs/tags/genome-3666
- refs/tags/genome-3667
- refs/tags/genome-3668
- refs/tags/genome-3669
- refs/tags/genome-3670
- refs/tags/genome-3671
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- refs/tags/genome-3673
- refs/tags/genome-3674
- refs/tags/genome-3675
- refs/tags/genome-3676
- refs/tags/genome-3677
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- refs/tags/genome-3814
Raw File
Take a new snapshot of a software origin
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Use the form below to proceed. Once a request has been submitted and accepted, it will be processed as soon as possible. You can then check its processing state by visiting this dedicated page.Processing "take a new snapshot" request ...
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Tip revision: 30e1a2f94a0dece01fd9f7c7b7d75531d60f1f70 authored by Chris Miller on 15 October 2012, 15:08:23 UTC
adding indel readcounts
adding indel readcounts
Tip revision: 30e1a2f
vm_builder.sh
#!/bin/bash
if [ "$UID" -ne "0" ]
then
echo "You must be root."
exit 1
fi
# set up genome repo
wget -O - -q http://repo.gsc.wustl.edu/ubuntu/files/genome-center.asc | sudo apt-key add -
cat <<EOF | sudo tee /etc/apt/sources.list.d/genome.list
deb http://repo.gsc.wustl.edu/ubuntu lucid main
deb http://repo.gsc.wustl.edu/ubuntu lucid-genome-development main
EOF
aptitude update
aptitude install -y git-core
aptitude install -y libur-perl
aptitude install -y libworkflow-perl
aptitude install -y libwebservice-solr-perl libcache-memcached-perl libtest-mockobject-perl bioperl libregexp-common-perl libmime-lite-perl libfile-grep-perl libfile-slurp-perl libinline-perl unzip libdatetime-perl
# refalign
aptitude install -y libfile-copy-recursive-perl
# Somatic
# get oracle-xe-universal_10.2.0.1-1.0_i386.deb
aptitude install -y libaio-dev libaio1
# gmt
aptitude install -y libsort-naturally-perl libanyevent-perl libtest-class-perl libexception-class-perl libmail-sender-perl libguard-perl libcarp-assert-perl libdatetime-perl libfile-ncopy-perl libmail-sendmail-perl libpoe-perl libpoe-component-ikc-perl libtext-csv-perl libmethod-alias-perl libmoosex-types-perl libnamespace-autoclean-perl libmoosex-types-path-class-perl libstatistics-basic-perl libmath-basecalc-perl libgtk2-perl libtest-output-perl libmoosex-strictconstructor-perl liblog-log4perl-perl liblog-dispatch-perl libdbix-dbschema-perl libdbix-class-schema-loader-perl libjson-perl libfile-copy-recursive-perl libgtk2.0-dev libgtk2.0-common cups-client default-jdk pari-gp libgraphics-gnuplotif-perl
aptitude install -y libtext-table-perl libemail-simple-perl libemail-valid-perl unzip weka
aptitude install -y pdl libplack-perl libfile-chdir-perl
# modules to cpan
# FASTAParse
# Class::DBI::Oracle
# modules that need manual install
# do we really need them?
# Math::Pari
# Inline::Java
# 1. Setup JAVA_HOME, then cpan Inline::Java may work
# setup bioperl
cd $HOME
mkdir build
cd $HOME/build
wget ftp://bioperl.org/pub/bioperl/DIST/bioperl-ext-1.5.1.tar.gz
tar bioperl-ext-1.5.1.tar.gz
cd bioperl-ext-1.5.1
perl Makefile.pl
cd $HOME/build
wget http://pari.math.u-bordeaux.fr/pub/pari/unix/pari-2.3.5.tar.gz
tar xvf pari-2.3*
wget http://search.cpan.org/CPAN/authors/id/I/IL/ILYAZ/modules/Math-Pari-2.01080605.tar.gz
tar xvf Math-Pari*
cd Math-Pari*
perl Makefile.pl
make
make install
# could run tests, but it wont make much difference