Bio-Linux

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.

The following packages are available in Bio-Linux 8, but absent from this PPA, as they are updated in

* 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

* Ubuntu 18.04 repos:

berkeley-express bitseq blimps jaligner king mothur parallel parsinsert pyqi rsem sickle sift treeviewx trinityrnaseq ugene yaggo

The following packages were removed from the Bionic release of this PPA, due to dependency problems:

beam2 ea-utils estscan2 galaxy-server-all jalview libbtlib-perl pass2 qiime* r-bioc-bitseq r-bioc-deseq r-bioc-edger r-bioc-hilbertvis r-bioc-pcamethods r-cran-abind r-cran-rcolorbrewer r-cran-samr r-cran-xtable

NOTES:

The package liboptimization-java was re-added to bionic, since 18.04 doesn't have it anymore.

The package hyphy-common is called hyphy in Bio-Linux 8. The latter should be removed if upgrading to Ubuntu 16.04/18.04, and hyphy-common installed instead.

The package blimps has not been removed from this PPA, due to blimps-data not existing in the Ubuntu 18.04 repos.

The package khmer has not been removed from this PPA, due to khmer-example and khmer-test not existing in the Ubuntu 16.04/18.04 repos.

The package paml has not been removed from this PPA, due to paml-data-extra not existing in the Ubuntu 16.04/18.04 repos.

The package staden-doc provides documentation for staden that doesn't exist in Ubuntu 16.04/18.04 repos.

MATE packages are not needed in this PPA. If you want to use MATE in Ubuntu, install Ubuntu MATE 16.04/18.04, or install ubuntu-mate-desktop on your existing 16.04/18.04 installation.

The Unity Scope for Bio-Linux 8 doesn't work in Ubuntu 18.04/16.04.

The marutter/c2d4u PPA has not ported the following packages to 18.04:

libhdf5-7 libicu52 r-cran-aplpack r-cran-gee r-cran-rwave r-cran-snowfall r-cran-waveslim r-cran-wavethresh

The following packages from marutter/c2d4u PPA were built for 18.04, but depend on r-api-3.4 (ie r-base-core 3.4.4) and thus can't be installed on Bionic until this dependency is solved:

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-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-bitops r-cran-catools r-cran-colorspace r-cran-dbi r-cran-dichromat r-cran-digest r-cran-evaluate r-cran-gdata r-cran-getopt r-cran-ggplot2 r-cran-gplots r-cran-gtable r-cran-gtools r-cran-labeling r-cran-leaps r-cran-lme4 r-cran-magrittr r-cran-matrixstats r-cran-minqa r-cran-munsell r-cran-nloptr r-cran-optparse 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-scales r-cran-scatterplot3d r-cran-snow r-cran-sp r-cran-stringi r-cran-stringr r-cran-tcltk2 r-cran-testthat r-cran-vegan r-cran-xml

ppa:x2go/stable has dependency problems on 18.04

=== 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:

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

On 16.04 run the following commands:

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: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: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

On 18.04 run the following commands instead:

apt-add-repository -y ppa:marutter/c2d4u
apt update
apt install icu-devtools libblas-dev libblas3 libicu-dev liblapack-dev liblapack3 libnlopt0 r-bioc-impute r-cran-boot r-cran-class r-cran-kernsmooth r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-permute r-cran-spatial r-cran-survival

apt-add-repository -y ppa:biohazara/bio-linux
apt update
apt install abyss acacia ampliconnoise bedtools blimps-data blimps-utils bowtie bowtie-examples bowtie2 bowtie2-examples bwa cdbfasta clearcut cufflinks emboss emboss-data emboss-doc emboss-lib emperor fasttree galaxy-server galaxy-server-test galaxy-tools-bl glam2 glimmer3 hyphy-common infernal infernal-doc jemboss jprofilegrid lastz libblimps3 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 perm pynast pyqi python-biom-format python-burrito python-burrito-fillings python-cogent python*-future python-natsort python-natsort-doc python-skbio python3-natsort r-bioc-qvalue r-bioc-zlibbioc r-cran-lattice r-cran-locfit r-cran-prettyr 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

Then on both distros run the following commands:

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-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-fasttree bio-linux-gap2caf bio-linux-glimmer3 bio-linux-hmmer 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-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-tree-puzzle bio-linux-treeview bio-linux-tutorials bio-linux-xcut bio-linux-zsh