From e474b8438b0fabe5b953fde4435ae5ba1dd0ea89 Mon Sep 17 00:00:00 2001 From: Pierre Pouchin Date: Tue, 29 Jan 2019 16:20:30 +0100 Subject: [PATCH 1/5] Added sRNAPipe recipe. --- recipes/srnapipe/1.1/build.sh | 3 +++ recipes/srnapipe/1.1/meta.yaml | 49 ++++++++++++++++++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 recipes/srnapipe/1.1/build.sh create mode 100644 recipes/srnapipe/1.1/meta.yaml diff --git a/recipes/srnapipe/1.1/build.sh b/recipes/srnapipe/1.1/build.sh new file mode 100644 index 0000000000000..e95df8f4665c1 --- /dev/null +++ b/recipes/srnapipe/1.1/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash +perl Makefile.PL +make install diff --git a/recipes/srnapipe/1.1/meta.yaml b/recipes/srnapipe/1.1/meta.yaml new file mode 100644 index 0000000000000..ffe86432b1293 --- /dev/null +++ b/recipes/srnapipe/1.1/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "srnapipe" %} +{% set version = "1.1" %} +{% set sha256 = "53186982956b7a4f2bfd35e3917f1c0be95c93b599fd05de0527a6482f4a046f" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/GReD-Clermont/perl-sRNAPipe/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl <5.23.0a0 + - perl-getopt-long + - perl-parallel-forkmanager + - perl-statistics-r + - perl-string-random + - perl-file-copy-recursive + - perl-math-cdf + run: + - perl <5.23.0a0 + - perl-getopt-long + - perl-parallel-forkmanager + - perl-statistics-r + - perl-string-random + - perl-file-copy-recursive + - perl-math-cdf + - r-base + - r-rcolorbrewer + - r-ggplot2 + - r-plotrix + - bioconductor-sushi + - bwa + - bedtools + - samtools 1.5.* + +test: + commands: + - sRNAPipe.pl + +about: + home: https://github.com/GReD-Clermont/perl-sRNAPipe + license: Academic Free License v3.0 + summary: Pipeline for bioinformatic in-depth exploration of small RNA-seq data From 66eaa31b36c3d191e55f0c06dbaee68e19e8e77a Mon Sep 17 00:00:00 2001 From: Pierre Pouchin Date: Tue, 29 Jan 2019 18:31:04 +0100 Subject: [PATCH 2/5] Updated tool dependencies versions. --- recipes/srnapipe/1.1/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/srnapipe/1.1/meta.yaml b/recipes/srnapipe/1.1/meta.yaml index ffe86432b1293..27c164465c84a 100644 --- a/recipes/srnapipe/1.1/meta.yaml +++ b/recipes/srnapipe/1.1/meta.yaml @@ -35,9 +35,9 @@ requirements: - r-ggplot2 - r-plotrix - bioconductor-sushi - - bwa - - bedtools - - samtools 1.5.* + - bwa >=0.7.12 + - bedtools >=2.24.0 + - samtools >=1.5 test: commands: From ad56075b94ed6b316a1da374a8d491ad9e8ebf88 Mon Sep 17 00:00:00 2001 From: Pierre Pouchin Date: Wed, 30 Jan 2019 13:38:04 +0100 Subject: [PATCH 3/5] Changed repo name --- recipes/srnapipe/1.1/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/srnapipe/1.1/meta.yaml b/recipes/srnapipe/1.1/meta.yaml index 27c164465c84a..c4b700c18dc78 100644 --- a/recipes/srnapipe/1.1/meta.yaml +++ b/recipes/srnapipe/1.1/meta.yaml @@ -1,13 +1,13 @@ {% set name = "srnapipe" %} {% set version = "1.1" %} -{% set sha256 = "53186982956b7a4f2bfd35e3917f1c0be95c93b599fd05de0527a6482f4a046f" %} +{% set sha256 = "c16bdbdea34f16f38f574b2b1d99cb7b1008e1feb56530d92210925308620265" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/GReD-Clermont/perl-sRNAPipe/archive/v{{ version }}.tar.gz + url: https://github.com/GReD-Clermont/sRNAPipe-cli/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} build: @@ -41,9 +41,9 @@ requirements: test: commands: - - sRNAPipe.pl + - srnapipe about: - home: https://github.com/GReD-Clermont/perl-sRNAPipe + home: https://github.com/GReD-Clermont/sRNAPipe-cli license: Academic Free License v3.0 summary: Pipeline for bioinformatic in-depth exploration of small RNA-seq data From 7bbd1588c570e3cd69c5872032e337d1f77ea495 Mon Sep 17 00:00:00 2001 From: Pierre Pouchin Date: Wed, 30 Jan 2019 15:24:59 +0100 Subject: [PATCH 4/5] Updated sha256 --- recipes/srnapipe/1.1/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/srnapipe/1.1/meta.yaml b/recipes/srnapipe/1.1/meta.yaml index c4b700c18dc78..b23c1b6b7e162 100644 --- a/recipes/srnapipe/1.1/meta.yaml +++ b/recipes/srnapipe/1.1/meta.yaml @@ -1,6 +1,6 @@ {% set name = "srnapipe" %} {% set version = "1.1" %} -{% set sha256 = "c16bdbdea34f16f38f574b2b1d99cb7b1008e1feb56530d92210925308620265" %} +{% set sha256 = "c1220a36e22e5403ced1633a32e3a60d394fbdf506a14e5b642a34fc81c2236b" %} package: name: {{ name }} From 5ada710bac6cf22a3a8245e52770acf6734084c8 Mon Sep 17 00:00:00 2001 From: Pierre Pouchin Date: Wed, 30 Jan 2019 16:42:28 +0100 Subject: [PATCH 5/5] Changed build to host --- recipes/srnapipe/1.1/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/srnapipe/1.1/meta.yaml b/recipes/srnapipe/1.1/meta.yaml index b23c1b6b7e162..52bed3532e68e 100644 --- a/recipes/srnapipe/1.1/meta.yaml +++ b/recipes/srnapipe/1.1/meta.yaml @@ -14,7 +14,7 @@ build: number: 0 requirements: - build: + host: - perl <5.23.0a0 - perl-getopt-long - perl-parallel-forkmanager