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| 1 | --- | |
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| 2 | # List of custom programs to install that are not packaged. These each require | |
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| 3 | # a install_name function in the appropriate place in the 'custom' directory to | |
| 4 | # define the steps for downloading, building, and installing the package. | |
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| 5 | bio_general: | |
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| 6 | #- bio4j # no easy download for 0.8 | |
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| 7 | - anaconda | |
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| 8 | - emboss | |
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| 9 | - pgdspider | |
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| 10 | bio_nextgen: | |
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| 11 | alignment: | |
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| 12 | - bowtie | |
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| 13 | - gmap | |
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| 14 | - lastz | |
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| 15 | - mosaik | |
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| 16 | # - perm # difficult build process with directory names | |
| 17 | - snap | |
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| 18 | #- stampy # no version names on tarballs | |
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| 19 | utilities: | |
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| 20 | - dwgsim | |
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| 21 | - fastq_screen | |
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| 22 | - ogap | |
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| 23 | - rnaseqc | |
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| 24 | - varianttools | |
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| 25 | - disambiguate | |
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| 26 | - alientrimmer | |
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| 27 | analysis: | |
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| 28 | # - echo # build problems on ubuntu 12.10 | |
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| 29 | - picard | |
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| 30 | - shrec | |
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| 31 | - tophat | |
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| 32 | - featurecounts | |
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| 33 | assembly: | |
| 34 | - abyss | |
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| 35 | - cortex_var | |
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| 36 | - ray | |
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| 37 | - transabyss | |
| 38 | - trinity | |
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| 39 | - velvet | |
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| 40 | sv: | |
| 41 | - hydra | |
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| 42 | - freec | |
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| 43 | variant: | |
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| 44 | - bcbio_variation | |
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| 45 | - crisp | |
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| 46 | - grabix | |
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| 47 | - mutect | |
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| 48 | - tassel | |
| 49 | - stacks | |
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| 50 | - varscan | |
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| 51 | chip: | |
| 52 | - macs | |
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| 53 | needs_64bit: | |
| 54 | - ucsc_tools | |
| 55 | - bfast | |
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| 56 | bio_proteomics: | |
| 57 | - transproteomic_pipeline | |
| 58 | - omssa | |
| 59 | - mzmine | |
| 60 | - myrimatch | |
| 61 | - directag | |
| 62 | - tagrecon | |
| 63 | - idpqonvert | |
| 64 | - pepitome | |
| 65 | - percolator | |
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| 66 | bio_proteomics_wine: | |
| 67 | - proteomics_wine_env | |
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| 68 | #- multiplierz | |
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| 69 | - proteowizard | |
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| 70 | - morpheus | |
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| 71 | cloudman: | |
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| 72 | - cloudman | |
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| 73 | - novnc | |
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| 74 | galaxy: | |
| 75 | - galaxy_webapp | |
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| 76 | galaxy_tools: | |
| 77 | - cbl_galaxy_tools | |
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| 78 | galaxyp: | |
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| 79 | - galaxy_protk | |
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| 80 | - protvis | |
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| 81 | # Pydoop and seal need update and should only be installed on cloud systems | |
| 82 | #distributed: | |
| 83 | # - pydoop | |
| 84 | # - seal | |
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| 85 | system: | |
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| 86 | - homebrew | |
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| 87 | - s3fs | |
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| 88 | python: | |
| 89 | - bx-python | |
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| 90 | - netsa-python | |
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| 91 | - rpy | |
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| 92 | java: | |
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| 93 | - leiningen | |
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| 94 | phylogeny: | |
| 95 | - tracer | |
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| 96 | - beast | |
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| 97 | #Viral Cloud Resource (VCR) - JCVI's Viral Genomic Pipelines on the cloud | |
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| 98 | vcr: | |
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| 99 | - galaxy_vcr | |
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| 100 | - viralassembly | |
| 101 | - viralassembly_cleanall | |
| 102 | - viralvigor | |
| 103 | - viralvigor_test | |
| 104 | - viralvigor_validate | |
| 105 | - viralvigor_cleanall | |
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| 106 | - vicvb | |
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| 107 | - vicvb_cleanall | |
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| 108 | # ToDo -- test on 64bit with bfast | |
| 109 | #- dnaa | |
| 110 | #- srma |