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# List of custom programs to install that are not packaged. These each require
# a install_name function in the appropriate place in the 'custom' directory to
# define the steps for downloading, building, and installing the package.
bio_general:
#- bio4j # no easy download for 0.8
- anaconda
- emboss
- pgdspider
bio_nextgen:
alignment:
- bowtie
- gmap
- lastz
- mosaik
# - perm # difficult build process with directory names
- snap
#- stampy # no version names on tarballs
utilities:
- dwgsim
- fastq_screen
- ogap
- rnaseqc
- varianttools
- disambiguate
- alientrimmer
analysis:
# - echo # build problems on ubuntu 12.10
- picard
- shrec
- tophat
- featurecounts
assembly:
- abyss
- cortex_var
- ray
- transabyss
- trinity
- velvet
sv:
- hydra
- freec
variant:
- bcbio_variation
- crisp
- grabix
- mutect
- tassel
- stacks
- varscan
chip:
- macs
needs_64bit:
- ucsc_tools
- bfast
bio_proteomics:
- transproteomic_pipeline
- omssa
- mzmine
- myrimatch
- directag
- tagrecon
- idpqonvert
- pepitome
- percolator
bio_proteomics_wine:
- proteomics_wine_env
#- multiplierz
- proteowizard
- morpheus
cloudman:
- cloudman
- novnc
galaxy:
- galaxy_webapp
galaxy_tools:
- cbl_galaxy_tools
galaxyp:
- galaxy_protk
- protvis
# Pydoop and seal need update and should only be installed on cloud systems
#distributed:
# - pydoop
# - seal
system:
- homebrew
- s3fs
python:
- bx-python
- netsa-python
- rpy
java:
- leiningen
phylogeny:
- tracer
- beast
#Viral Cloud Resource (VCR) - JCVI's Viral Genomic Pipelines on the cloud
vcr:
- galaxy_vcr
- viralassembly
- viralassembly_cleanall
- viralvigor
- viralvigor_test
- viralvigor_validate
- viralvigor_cleanall
- vicvb
- vicvb_cleanall
# ToDo -- test on 64bit with bfast
#- dnaa
#- srma
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