Bio-Linux

PPA description

The packages provided by this PPA are a binary copy from https://launchpad.net/~nebc/+archive/ubuntu/bio-linux?field.series_filter=trusty and are NOT TESTED. I'll attempt to build and update them after Ubuntu 18.04 comes out.

The following packages are available in Bio-Linux 8, but absent from this PPA, as they are updated in the Ubuntu 16.04 repos:

abyss ampliconnoise arb bamtools bedtools bowtie bowtie-examples bowtie2 bowtie2-examples bwa clearcut duplicity duply ea-utils emboss emboss-data emboss-doc emboss-lib emboss-test fasttree hyphy-common infernal jellyfish jellyfish-examples jemboss khmer khmer-example khmer-test libcolt-free-java libcolt-free-java-doc librdp-taxonomy-tree-java libsis-base-java mafft mira-assembler mira-examples mira-doc ncbi-seg parafly paramiko perm pymol python-biom-format python-boto python-burrito python-cogent python-cogent-doc python-future python3-future python-screed python3-boto python-natsort python-natsort-doc python3-natsort python-setproctitle python3-setproctitle python-paramiko python3-paramiko python-pandas python-pandas-doc python-sortedcontainers python3-sortedcontainers raxml ray ray-doc ray-extra r-cran-abind r-cran-lattice r-cran-rcolorbrewer ruby-colorize scythe seqprep sortmerna stacks stacks-web staden staden-common sumatra swarm tcode tophat transdecoder velvet velvet-example velvet-long velvetoptimiser vsearch

NOTES:

The package hyphy-common is called hyphy in Bio-Linux 8. The latter should be removed if upgrading to Ubuntu 16.04, and hyphy-common installed instead.

The package paml has not been removed from this PPA, due to paml-data-extra not existing in the Ubuntu 16.04 repos.

The package staden-doc provides documentation for staden that doesn't exist in Ubuntu 16.04 repos.

MATE packages are not needed in this PPA. If you want to you MATE in Ubuntu, install Ubuntu MATE 16.04, or install ubuntu-mate-desktop on your existing 16.04 installation.

The Unity Scope for Bio-Linux 8 doesn't work in Ubuntu 16.04.

=== WARNING, INSTRUCTIONS NOT TESTED ==

Here's how to install all packages necessary to have the same packages installed by default as Bio-Linux 8 on Ubuntu 16.04:

First, you need to install the official R repo at https://cran.r-project.org/bin/linux/ubuntu/README.html. Only then you are ready to install by following these commands:

sudo -s
apt update
apt install python-rpy python-rpy-doc python-rpy2 r-base r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-doc-info r-doc-pdf r-mathlib r-recommended

apt-add-repository -y ppa:biohazara/bio-linux
apt update
apt install abyss acacia ampliconnoise beam2 bedtools blimps-data blimps-utils bowtie bowtie-examples bowtie2 bowtie2-examples bwa cdbfasta clearcut cufflinks ea-utils emboss emboss-data emboss-doc emboss-lib emperor estscan2 fasttree galaxy-server galaxy-server-all galaxy-server-test galaxy-tools-bl glam2 glimmer3 hyphy-common infernal infernal-doc jalview jemboss jprofilegrid lastz libblimps3 libbtlib-perl libcaja-extension1 libcolt-free-java libdsol1-java libhac-java libjaba-client-java libjdas-java liboptimization-java libpandaseq-sam1 libpandaseq5 librdp-readseq-java librdp-taxonomy-tree-java libssj-java libvarna-java lucy macs14 mafft mdust meme meme-examples mira-3rdparty mothur natefoo-add-scores natefoo-taxonomy oswitch paml paml-data-extra paml-doc pandaseq pandaseq-sam parallel parsinsert pass2 perm pynast pyqi python-biom-format python-burrito python-burrito-fillings python-cogent python-future python-natsort python-natsort-doc python-skbio python3-natsort qiime qiime-data qiime-default-reference qiime-doc r-bioc-bitseq r-bioc-deseq r-bioc-edger r-bioc-hilbertvis r-bioc-pcamethods r-bioc-qvalue r-bioc-zlibbioc r-cran-lattice r-cran-locfit r-cran-prettyr r-cran-samr r-cran-xtable raxml rdp-classifier rdp-classifier-doc ruby-colorize runurl seqprep sift sortmerna sputnik-mononucleotide stacks staden staden-common staden-doc sumatra swarm tcode tophat treeviewx trnascan-se velvet velvet-example velvet-long vsearch weblogo

apt-add-repository -y ppa:marutter/c2d4u
apt update
apt install icu-devtools libblas-dev libblas3 libhdf5-7 libicu-dev libicu52 liblapack-dev liblapack3 libnlopt0 r-bioc-affy r-bioc-affyio r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocinstaller r-bioc-biostrings r-bioc-genefilter r-bioc-geneplotter r-bioc-genomeinfodb r-bioc-genomicranges r-bioc-impute r-bioc-iranges r-bioc-limma r-bioc-multtest r-bioc-preprocesscore r-bioc-rsamtools r-bioc-s4vectors r-bioc-xvector r-cran-abind r-cran-ade4 r-cran-ape r-cran-aplpack r-cran-bitops r-cran-boot r-cran-catools r-cran-class r-cran-colorspace 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-kernsmooth r-cran-labeling r-cran-leaps r-cran-lme4 r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mgcv r-cran-minqa r-cran-munsell r-cran-nlme r-cran-nloptr r-cran-nnet r-cran-optparse r-cran-permute r-cran-plotrix r-cran-plyr r-cran-proto r-cran-r.methodss3 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppeigen r-cran-rcurl r-cran-relimp r-cran-reshape2 r-cran-rggobi r-cran-rgl r-cran-rgtk2 r-cran-rmpi r-cran-rserve r-cran-rsqlite r-cran-rwave r-cran-scales r-cran-scatterplot3d r-cran-snow r-cran-snowfall r-cran-sp r-cran-spatial r-cran-stringi r-cran-stringr r-cran-survival r-cran-tcltk2 r-cran-testthat r-cran-vegan r-cran-waveslim r-cran-wavethresh r-cran-xml

apt-add-repository -y ppa:x2go/stable
apt update
apt install libnx-x11-6 libnx-xcomposite1 libnx-xdamage1 libnx-xdmcp6 libnx-xext6 libnx-xfixes3 libnx-xpm4 libnx-xrandr2 libnx-xrender1 libnx-xtst6 libssh-4 libxcomp3 libxcompext3 libxcompshad3 nx-x11-common nxagent nxproxy unity-greeter x2goagent x2goclient x2goserver x2goserver-extensions x2goserver-xsession

wget https://github.com/Bio-Linux/build-bio-linux/raw/master/upgrade_to_8/bio-linux-keyring_7_all.deb

dpkg -EGi ./bio-linux-keyring_7_all.deb

tee -a /etc/apt/sources.list.d/bio-linux-legacy.list <<EOF
# Bio-Linux legacy packages (manually built, there is no deb-src)
# But there is an alternative mirror you can use.
# deb http://distro.ibiblio.org/bio-linux/packages/ unstable bio-linux
deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux
EOF

apt update
apt install bio-linux-ampliconnoise bio-linux-arb 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-cruft-killer 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 bio-linux-hmmer bio-linux-jalview bio-linux-jmotu bio-linux-jprofilegrid bio-linux-keyring bio-linux-lucy 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-plymouth-theme 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-shared bio-linux-splitstree bio-linux-squint bio-linux-staden bio-linux-stars bio-linux-t-coffee bio-linux-tablet bio-linux-taxinspector 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

Adding this PPA to your system

You can update your system with unsupported packages from this untrusted PPA by adding ppa:biohazara/bio-linux to your system's Software Sources. (Read about installing)

sudo add-apt-repository ppa:biohazara/bio-linux
sudo apt-get update
        
Technical details about this PPA

This PPA can be added to your system manually by copying the lines below and adding them to your system's software sources.

deb http://ppa.launchpad.net/biohazara/bio-linux/ubuntu xenial main 
deb-src http://ppa.launchpad.net/biohazara/bio-linux/ubuntu xenial main 
Signing key:
4096R/A93F3E1EB808874957870AF6D440FC584AFEA7CB (What is this?)
Fingerprint:
A93F3E1EB808874957870AF6D440FC584AFEA7CB

For questions and bugs with software in this PPA please contact biohazara.

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Overview of published packages

175 of 103 results
Package Version Uploaded by
acacia 1.53-0biolinux2 Tim Booth (2017-12-01)
annotate 1.42.0-0biolinux1 Tim Booth (2017-12-01)
annotationdbi 1.26.0-0biolinux1 Tim Booth (2017-12-01)
axiome 1.7biolinux1 Tim Booth (2017-12-01)
beam2 0.1+20101008-1biolinux1.1 Tim Booth (2017-12-01)
berkeley-express 1.5.1-1biolinux1 Tim Booth (2017-12-01)
biobase 2.28.0-1cran1ppa0 Michael Rutter (2017-12-01)
biocgenerics 0.14.0-1cran1ppa0 Michael Rutter (2017-12-01)
biocparallel 1.2.9-1cran1ppa0 Michael Rutter (2017-12-01)
biostrings 2.36.4-2biolinux1 Tim Booth (2017-12-01)
bitseq 0.7.0-0biolinux1.1 Tim Booth (2017-12-01)
blimps 3.9-2biolinux1 Tim Booth (2017-12-01)
btlib 0.19-1biolinux0.1 Tim Booth (2017-12-01)
cdbfasta 20100722-2biolinux0.1 Tim Booth (2017-12-01)
cortex-con 0.05-1biolinux0.1 Tim Booth (2017-12-01)
data.table 1.9.4-1cran1ppa0trusty0 Michael Rutter (2017-12-01)
deseq 1.16.0-0biolinux2 Tim Booth (2017-12-01)
edger 3.6.2-0biolinux2 Tim Booth (2017-12-01)
estscan2 2.1-2biolinux1.1 Tim Booth (2017-12-01)
fraggenescan 1.19-0biolinux1 Tim Booth (2017-12-01)
futile.logger 1.4.1-1cran1ppa0 Michael Rutter (2017-12-01)
futile.options 1.0.0-1cran1precise3 Michael Rutter (2017-12-01)
galaxy 1.bl.py27.20140730-0biolinux3 Tim Booth (2017-12-01)
galaxy-tools-bl 1:0.5.1 Tim Booth (2017-12-01)
genefilter 1.46.1-0biolinux2 Tim Booth (2017-12-01)
geneplotter 1.42.0-0biolinux2 Tim Booth (2017-12-01)
genomicalignments 1.4.1-2biolinux1 Tim Booth (2017-12-01)
genomicranges 1.20.6-2biolinux2 Tim Booth (2017-12-01)
glimmer3 3.02-4biolinux2.1 Tim Booth (2017-12-01)
gnx-tools 0.1+20120305-3biolinux1.2 Tim Booth (2017-12-01)
hilbertvis 1.23.0-0biolinux1 Tim Booth (2017-12-01)
impute 1.38.1-0biolinux1 Tim Booth (2017-12-01)
iranges 2.2.7-2biolinux1 Tim Booth (2017-12-01)
jaligner 1.0+dfsg-1biolinux1 Tim Booth (2017-12-01)
jalview 2.8.0b1.dfsg-0biolinux1.1 Tim Booth (2017-12-01)
jprofilegrid 2.0.5-1biolinux0.1 Tim Booth (2017-12-01)
king 2.21.120420+repack-3biolinux0.1 Tim Booth (2017-12-01)
lambda.r 1.1.7-1cran1ppa0 Michael Rutter (2017-12-01)
lastz 1.02.00-3biolinux1.1 Tim Booth (2017-12-01)
libdsol1-java 1.6.9-0biolinux4 Tim Booth (2017-12-01)
libjaba-client-java 2.0.1-0biolinux3.1 Tim Booth (2017-12-01)
libjung-java 2.0.1-1biolinux1 Tim Booth (2017-12-01)
librdp-alignment-java 0.1.20140606-0biolinux1 Tim Booth (2017-12-01)
librdp-readseq-java 0.1.20150512-0biolinux1 Tim Booth (2017-12-01)
libssj-java 2.5-1biolinux1 Tim Booth (2017-12-01)
limma 3.20.5-0biolinux1 Tim Booth (2017-12-01)
locfit 1.5-9.1-1cran1.2 Tim Booth (2017-12-01)
lucy 1.19p-1biolinux0.1 Tim Booth (2017-12-01)
macs14 1.4.2.1-0biolinux1 Tim Booth (2017-12-01)
matrixstats 0.10.0-0biolinux1 Tim Booth (2017-12-01)
mdust 1:0.1+20020708-2biolinux1.1 Tim Booth (2017-12-01)
meme 1:4.10.0.1-0ubuntu2 Tim Booth (2017-12-01)
metavelvet 1.2.02-0biolinux1 Tim Booth (2017-12-01)
mira-3rdparty 20120706-1biolinux0.1 Tim Booth (2017-12-01)
mothur 1.36.1+dfsg-0biolinux1 Tim Booth (2017-12-01)
mothur-lookup-files 1-0biolinux2 Tim Booth (2017-12-01)
natefoo-add-scores 0.1+20101006-3biolinux1.1 Tim Booth (2017-12-01)
natefoo-taxonomy 0.1+20101102-2biolinux1.1 Tim Booth (2017-12-01)
openmotif 2.3.4-0biolinux3 Tim Booth (2017-12-01)
optparse 1.2.0-1cran1trusty0 Michael Rutter (2017-12-01)
oswitch 0.2.6 Anuarg Priyam (2017-12-01)
paml 4.7-1biolinux1 (Newer version available) Tim Booth (2017-12-01)
panama 0.4-0biolinux4.1 Tim Booth (2017-12-01)
pandaseq 2.7~ppa0 Andre Masella (2017-12-01)
pandaseq-sam 1.2~ppa0 Andre Masella (2017-12-01)
parallel 20150422-0biolinux1 Tim Booth (2017-12-01)
parsinsert 1.04-1biolinux1.1 Tim Booth (2017-12-01)
pass2 0.1+20101008-3biolinux1.1 Tim Booth (2017-12-01)
pcamethods 1.54.0-0biolinux1 Tim Booth (2017-12-01)
prettyr 2.0-8-0ubuntu1 Tim Booth (2017-12-01)
propcis 0.2-5-0ubuntu1 Tim Booth (2017-12-01)
pyqi 0.3.2+dfsg-1biolinux1 Tim Booth (2017-12-01)
python-burrito-fillings 0.1.1-0biolinux1 Tim Booth (2017-12-01)
python-emperor 0.9.51-0biolinux1 Tim Booth (2017-12-01)
python-intervaltree 2.1.0-2biolinux1 Tim Booth (2017-12-01)
175 of 103 results

Latest updates

  • s4vectors 42 weeks ago
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