Single-file installation of a basic set of bioinformatics tools, using cloudbiolinux.

deploy.sh

#!/bin/bash
set -e
set -o pipefail

# All-in-one installation script to download, configure, and run cloudbiolinux
# to install bioinformatics tools locally without needing sudo. The executables
# will go into $INSTALL_DIR:
INSTALL_DIR=~/tmp/cbl_demo

# See https://github.com/chapmanb/cloudbiolinux for more info on customizing
# installations.


pip install fabric
git clone https://github.com/chapmanb/cloudbiolinux
cd cloudbiolinux
HERE=$(pwd)
LCDB=${HERE}/contrib/flavor/lcdb

mkdir -p $LCDB && cd $LCDB

#
# "here documents" are used to write config files to a new cloudbiolinux flavor
# called "lcdb".
#
# This one creates the config file used by cloudbiolinux to tell it where to
# install the binaries.
cat > fabricrc.txt << EOF
# Global installation directory for packages and standard programs
system_install = ${INSTALL_DIR}

# Local install directory for versioned software that will not
# be included in the path by default
local_install = ~${INSTALL_DIR}/share

# Global setting for using sudo; allows installation of custom packages
# by non-privileged users.
# *Note*: ``system_install`` needs to point to a user-writeable directory if
# ``use_sudo`` is set to ``False``
use_sudo = False
keep_isolated = True

# -- Details about reference data installation
# Path where biological reference data files should be retrieved to
data_files = ${INSTALL_DIR}/biodata
EOF


# See https://github.com/chapmanb/cloudbiolinux/tree/master/config for what
# packages are available.  Here we're overriding the files to have a much
# smaller download footprint.
cat > custom.yaml << EOF
---
bio_nextgen:
    analysis:
        - picard
        - tophat
        - featurecounts
    needs_64bit:
        - ucsc_tools
EOF

cat > main.yaml << EOF
---
packages:
  - minimal
  - libraries
  - python
  - java
  - ruby
  - bio_nextgen
EOF

cat > packages-homebrew.yaml << EOF
---
bio_nextgen:
    alignment:
        - bwa
        - bowtie2
        - novoalign
        - rna-star
    utilities:
        - bamtools
        - bedtools
        - fastqc
    analysis:
        - samtools
        - cufflinks-binary
        - htslib
        - bcftools
EOF


# Change back to the top dir of the repository and run the fabfile, telling it
# to use the newly-configured "lcdb" flavor.
cd ${HERE}
fab -f fabfile.py -H localhost install_biolinux:flavor=lcdb