| 1 | # -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4 |
|---|
| 2 | # $Id$ |
|---|
| 3 | |
|---|
| 4 | PortSystem 1.0 |
|---|
| 5 | PortGroup github 1.0 |
|---|
| 6 | |
|---|
| 7 | github.setup BenLangmead bowtie2 c614bc1 |
|---|
| 8 | |
|---|
| 9 | name bowtie2 |
|---|
| 10 | version 2.2.9 |
|---|
| 11 | categories science biology |
|---|
| 12 | platforms darwin |
|---|
| 13 | license GPL-3 |
|---|
| 14 | maintainers mit.edu:gaberoo \ |
|---|
| 15 | openmaintainer |
|---|
| 16 | description Bowtie 2: Fast and sensitive read alignment |
|---|
| 17 | long_description Bowtie 2 is an ultrafast and memory-efficient tool \ |
|---|
| 18 | for aligning sequencing reads to long reference \ |
|---|
| 19 | sequences. It is particularly good at aligning reads \ |
|---|
| 20 | of about 50 up to 100s or 1,000s of characters, and \ |
|---|
| 21 | particularly good at aligning to relatively long \ |
|---|
| 22 | (e.g. mammalian) genomes. Bowtie 2 indexes the genome \ |
|---|
| 23 | with an FM Index to keep its memory footprint small: \ |
|---|
| 24 | for the human genome, its memory footprint is \ |
|---|
| 25 | typically around 3.2 GB. Bowtie 2 supports gapped, \ |
|---|
| 26 | local, and paired-end alignment modes. |
|---|
| 27 | homepage http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
|---|
| 28 | checksums rmd160 8fed27ccd9bf356e4fe0af24c83deff4fa798fa8 \ |
|---|
| 29 | sha256 23bcdee50fda50ea22286574fe314b2edbc1fd4f3bcae30ea8109c1d2a87752f |
|---|
| 30 | |
|---|
| 31 | patchfiles patch-src-Makefile.diff |
|---|
| 32 | |
|---|
| 33 | use_configure no |
|---|
| 34 | universal_variant no |
|---|
| 35 | |
|---|
| 36 | build.args-append CC=${configure.cc} \ |
|---|
| 37 | CXX=${configure.cxx} \ |
|---|
| 38 | CPP=${configure.cpp} |
|---|
| 39 | |
|---|
| 40 | destroot { |
|---|
| 41 | xinstall -m 755 -W ${worksrcpath} \ |
|---|
| 42 | bowtie2 \ |
|---|
| 43 | bowtie2-align-s \ |
|---|
| 44 | bowtie2-align-l \ |
|---|
| 45 | bowtie2-build \ |
|---|
| 46 | bowtie2-build-s \ |
|---|
| 47 | bowtie2-build-l \ |
|---|
| 48 | bowtie2-inspect \ |
|---|
| 49 | bowtie2-inspect-s \ |
|---|
| 50 | bowtie2-inspect-l \ |
|---|
| 51 | ${destroot}${prefix}/bin |
|---|
| 52 | |
|---|
| 53 | xinstall -m 755 -d ${destroot}${prefix}/share/doc/${name} |
|---|
| 54 | xinstall -m 644 -W ${worksrcpath} \ |
|---|
| 55 | VERSION \ |
|---|
| 56 | TUTORIAL \ |
|---|
| 57 | README \ |
|---|
| 58 | NEWS \ |
|---|
| 59 | MANUAL.markdown \ |
|---|
| 60 | MANUAL \ |
|---|
| 61 | LICENSE \ |
|---|
| 62 | AUTHORS \ |
|---|
| 63 | ${destroot}${prefix}/share/doc/${name} |
|---|
| 64 | } |
|---|
