Bio-Linux vs Debian-Med package lists [update]
Hi, Andreas.
Re: Our discussion at the 2018 Debian-Med Sprint in Barcelona.
I've compared our Bio-Linux 'master' package list used to create the
'live/install' USB stick with your "med-bio*" list of 'Recommends:'.
Updated to remove ',' from the end of "med-bio*" package names and the
"bio-linux-" prefix from the Bio-Linux 'master' package list.
Bye,
Tony.
--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548 http://minke-informatics.co.uk
mob. +44(0)7985 078324 mailto:tony.travis@minke-informatics.co.uk
--- bl_package_list.txt 2018-02-11 19:10:52.727650855 +0100
+++ debian-med-bio.list 2018-02-11 19:13:54.551645483 +0100
@@ -1,319 +1,544 @@
+abacas
abyss
acacia
-apache2
-archaeopteryx
+acedb-other
+adapterremoval
+adun-core
+aegean
+aevol
+alien-hunter
+alter-sequence-alignment
+amap-align
+amos-assembler
+amoscmp
+ampliconnoise
+andi
+apollo
+arachne
+aragorn
+arb
+ariba
artemis
-assembly-conversion-tools
-backups
-beam2
+asap
+atac
+augustus
+autodock
+autodocktools
+autodock-vina
+autogrid
+avogadro
+axe-demultiplexer
+axparafit
+bagpipe
+baitfisher
+ballview
+bambus
+bandage
+barrnap
+beads
+beagle
+bedops
+biceps
big-blast
+bigsdb
+bioclipse
+bio-eagle
bioperl
-bioperl-run
biosquid
-blast
-bldp-files
+bitseq
+blasr
+blat
blimps-utils
blixem
+blobology
bowtie
-bowtie2
-bowtie2-examples
-bowtie-examples
+boxshade
+bppsuite
+btk-core
bwa
-cap3
-catchall
+cactus
+caftools
+card-rgi
+cassiopee
+ccs
cdbfasta
cd-hit
-chimeraslayer
-chkrootkit
-cifs-utils
-clustal
-cmake
-cufflinks
-curl
-cython
-cython-dbg
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+cellprofiler
+centrifuge
+cgview
+cinema
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+circos
+clearcut
+clonalframe
+clonalorigin
+cluster3
+cmap
+cnvkit
+codonw
+compclust
+concavity
+condetri
+conservation-code
+contrafold
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+coot
+copycat
+crossbow
+crux-toolkit
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cytoscape
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emboss
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fasta
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fasttree
fastx-toolkit
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glam2
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-hyphy
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jalview
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jellyfish
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-libapache2-reload-perl
-libapache-dbi-perl
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libbiojava-java
-libbiojava-java-demos
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-libdbd-pg-perl
-libio-string-perl
-libmailtools-perl
-libspreadsheet-parseexcel-perl
-libspreadsheet-writeexcel-perl
-libtext-csv-perl
+libbio-mage-perl
+libbio-mage-utils-perl
+libbio-primerdesigner-perl
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+libfast5-dev
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+libfreecontact-dev
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lucy
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mafft
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meme
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mesquite
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msatfinder
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mview
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oligoarrayaux
omegamap
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perm
pfaat
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picard-tools
-postgresql
-postgresql-client
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prank
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predictprotein
-priam
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pynast
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-python-biopython-doc
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-python-rpy2
-python-rpy-doc
-python-scipy
-qiime
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qtlcart
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raxml
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-r-bioc-annotationdbi
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r-bioc-biobase
-r-bioc-biocgenerics
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-r-bioc-deseq
-r-bioc-edger
-r-bioc-genefilter
-r-bioc-geneplotter
-r-bioc-genomicranges
+r-bioc-cummerbund
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r-bioc-hilbertvis
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r-bioc-limma
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-r-bioc-preprocesscore
-r-bioc-qvalue
-r-bioc-rsamtools
-r-bioc-zlibbioc
+r-bioc-mergeomics
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rbs-finder
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r-cran-ape
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r-cran-vegan
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-r-doc-html
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seqan-apps
seqan-dev
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sift
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splitstree
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staden
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taxinspector
tetra
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tophat
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transtermhp
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trnascan-se
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ugene
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abyss
acacia
ampliconnoise
apache2
beam2
bio-linux-ampliconnoise
bio-linux-archaeopteryx
bio-linux-artemis
bio-linux-assembly-conversion-tools
bio-linux-backups
bio-linux-big-blast
bio-linux-blast
bio-linux-bldp-files
bio-linux-blixem
bio-linux-cap3
bio-linux-catchall
bio-linux-cd-hit
bio-linux-clustal
bio-linux-cytoscape
bio-linux-dendroscope
bio-linux-dotter
bio-linux-dust
bio-linux-emboss
bio-linux-fasta
bio-linux-fastdnaml
bio-linux-fastqc
bio-linux-fasttree
bio-linux-gap2caf
bio-linux-glimmer3
bio-linux-happy:i386
bio-linux-hmmer
bio-linux-jmotu
bio-linux-jprofilegrid
bio-linux-keyring
bio-linux-lucy
bio-linux-mate-desktop
bio-linux-mcl
bio-linux-mesquite
bio-linux-mira
bio-linux-mira-3rd-party
bio-linux-mothur
bio-linux-mrbayes
bio-linux-msatfinder
bio-linux-mspcrunch
bio-linux-mummer
bio-linux-muscle
bio-linux-mview
bio-linux-ncbi-tools-x11
bio-linux-njplot
bio-linux-nrdb
bio-linux-ocount
bio-linux-oligoarray
bio-linux-oligoarrayaux
bio-linux-omegamap
bio-linux-paml
bio-linux-pfaat
bio-linux-phylip
bio-linux-phyml
bio-linux-priam
bio-linux-primer3
bio-linux-qiime
bio-linux-qtlcart
bio-linux-rasmol
bio-linux-rbs-finder
bio-linux-rdp-classifier
bio-linux-readseq
bio-linux-sampledata
bio-linux-samtools
bio-linux-splitstree
bio-linux-squint
bio-linux-staden
bio-linux-stars
bio-linux-tablet
bio-linux-taxinspector
bio-linux-t-coffee
bio-linux-tetra
bio-linux-themes-v8
bio-linux-tree-puzzle
bio-linux-treeview
bio-linux-tutorials
bio-linux-usb-maker
bio-linux-xcut
bio-linux-zsh
bioperl
bioperl-run
biosquid
blimps-utils
bowtie
bowtie2
bowtie2-examples
bowtie-examples
bwa
cdbfasta
chimeraslayer
chkrootkit
cifs-utils
cmake
cufflinks
curl
cython
cython-dbg
debconf
default-jdk
dialign
dictionaries-common
eclipse
emacs
emacsen-common
emacs-goodies-el
estscan2
evince
evolution
evolution-indicator
fastdnaml
fastjar
fastx-toolkit
g++
galaxy-server-all
gcc
gedit
gfortran
gimp
glam2
gnome-session-fallback*
gnuplot
graphicsmagick
graphviz
hmmer
hyphy
icedtea-7-plugin
indicator-applet-complete
jalview
jellyfish
jemboss
last-align
lastz
less
libapache2-reload-perl
libapache-dbi-perl
libbiojava-java
libbiojava-java-demos
libc6-dev
libconfig-simple-perl
libdata-stag-perl
libdbd-pg-perl
libio-string-perl
libmailtools-perl
libspreadsheet-parseexcel-perl
libspreadsheet-writeexcel-perl
libtext-csv-perl
lynx
mafft
make
maq
mcl
mdadm
meld
meme
meme-examples
microbiomeutil
mira-3rdparty
mira-assembler
mira-doc
mira-examples
mothur
mrbayes
mummer
muscle
mysql-client
ncbi-tools-bin
njplot
openjdk-7-jdk
openjdk-7-jre
openmpi-bin
openmpi-common
openssh-server
oswitch
paml
parallel
pass2
patch
perl
perl-doc
perl-modules
perl-tk
perm
pgadmin3
phylip
phyml
picard-tools
postgresql
postgresql-client
prank
predictprotein
primer3
probcons
pynast
python
python-all-dev
python-biopython
python-biopython-doc
python-biopython-sql
python-cogent
python-rpy
python-rpy2
python-rpy-doc
python-scipy
rasmol
raxml
r-base
r-base-core
r-base-dev
r-base-html
r-bioc-affy
r-bioc-affyio
r-bioc-annotate
r-bioc-annotationdbi
r-bioc-biobase
r-bioc-biocgenerics
r-bioc-biocinstaller
r-bioc-biomart
r-bioc-biostrings
r-bioc-bitseq
r-bioc-deseq
r-bioc-edger
r-bioc-genefilter
r-bioc-geneplotter
r-bioc-genomicranges
r-bioc-hilbertvis
r-bioc-impute
r-bioc-iranges
r-bioc-limma
r-bioc-multtest
r-bioc-pcamethods
r-bioc-preprocesscore
r-bioc-qvalue
r-bioc-rsamtools
r-bioc-zlibbioc
r-cran-abind
r-cran-ade4
r-cran-ape
r-cran-aplpack
r-cran-bitops
r-cran-catools
r-cran-cluster
r-cran-dbi
r-cran-dichromat
r-cran-digest
r-cran-evaluate
r-cran-gdata
r-cran-gee
r-cran-getopt
r-cran-ggplot2
r-cran-gplots
r-cran-gtable
r-cran-gtools
r-cran-labeling
r-cran-lattice
r-cran-leaps
r-cran-lme4
r-cran-locfit
r-cran-matrix
r-cran-matrixstats
r-cran-munsell
r-cran-nlme
r-cran-optparse
r-cran-permute
r-cran-plotrix
r-cran-plyr
r-cran-prettyr
r-cran-proto
r-cran-rcolorbrewer
r-cran-rcpp
r-cran-rcurl
r-cran-relimp
r-cran-reshape2
r-cran-rggobi
r-cran-rgl
r-cran-rgtk2
r-cran-r.methodss3
r-cran-rmpi
r-cran-rserve
r-cran-rsqlite
r-cran-rwave
r-cran-samr
r-cran-scales
r-cran-scatterplot3d
r-cran-snow
r-cran-snowfall
r-cran-sp
r-cran-stringr
r-cran-tcltk2
r-cran-testthat
r-cran-vegan
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