From 98940f766a3dfb18026cd4e74b31cdc75e40321d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Mon, 23 Jul 2018 15:52:04 +0200 Subject: [PATCH 01/12] gembs: passes a mulled build --- recipes/gem3-mapper/gemBS_conda_v1/build.sh | 12 ++++ recipes/gem3-mapper/gemBS_conda_v1/meta.yaml | 35 +++++++++++ recipes/gembs/build.sh | 6 ++ recipes/gembs/meta.yaml | 63 ++++++++++++++++++++ 4 files changed, 116 insertions(+) create mode 100644 recipes/gem3-mapper/gemBS_conda_v1/build.sh create mode 100644 recipes/gem3-mapper/gemBS_conda_v1/meta.yaml create mode 100644 recipes/gembs/build.sh create mode 100644 recipes/gembs/meta.yaml diff --git a/recipes/gem3-mapper/gemBS_conda_v1/build.sh b/recipes/gem3-mapper/gemBS_conda_v1/build.sh new file mode 100644 index 0000000000000..d325e176e8aa2 --- /dev/null +++ b/recipes/gem3-mapper/gemBS_conda_v1/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#adding include and library paths in order to find bzip2 +sed -i.bak ' + /^PATH_INCLUDE=/ s@$@ -I'$PREFIX'/include@ + /^PATH_LIB=/ s@$@ -L'$PREFIX'/lib@ + ' Makefile.mk.in + +./configure +make all +mkdir -p $PREFIX/bin +cp bin/* $PREFIX/bin diff --git a/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml b/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml new file mode 100644 index 0000000000000..c608f3a6ffc11 --- /dev/null +++ b/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "gemBS_conda_v1" %} +{% set sha256 = "3193250629bcf4567b832c5de3303e676d4a82bcdf84fecf24d2f7b2ab4398be" %} + +package: + name: gem3-mapper + version: {{ version }} + +source: + url: https://github.com/karl616/gem3-mapper/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - {{ compiler('c') }} + host: + - bzip2 + - zlib + run: + - bzip2 + - zlib + +test: + commands: + - gem-mapper 2>&1 | grep 'index|-I ' + - gem-indexer -h 2>&1 | grep 'input|-i (Multi-FASTA)' + - gem-retriever -h 2>&1 | grep 'index|-I (GEM archive)' + +about: + home: https://github.com/smarco/gem3-mapper + license: GPL3 + summary: The GEM read mapper (v3). + diff --git a/recipes/gembs/build.sh b/recipes/gembs/build.sh new file mode 100644 index 0000000000000..a078ced4005e2 --- /dev/null +++ b/recipes/gembs/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +#instead of installing software from submodules, let them be dependencies + +$PYTHON setup.py install --minimal + diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml new file mode 100644 index 0000000000000..2d7e5d0238d8a --- /dev/null +++ b/recipes/gembs/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "conda_v2" %} +{% set sha256 = "1ead3f20a36a40c0737ec58c2e783b9c1cb6a9de0317c0009964d1b164c598a0" %} +{% set bcftoolsversion = "1.8" %} +{% set bcftoolssha256 = "4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced"%} + +package: + name: gembs + version: {{ version }} + +source: + - url: https://github.com/karl616/gemBS/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + - url: https://github.com/samtools/bcftools/releases/download/{{ bcftoolsversion }}/bcftools-{{ bcftoolsversion }}.tar.bz2 + sha256: {{ bcftoolssha256 }} + folder: tools/bcftools + +build: + number: 0 + skip: True # [py27] + +requirements: + build: + - {{ compiler('c') }} + host: + - python >=3.0 + - zlib + - bzip2 + - xz + - htslib =1.8 + - ncurses + - matplotlib + - multiprocess + - curl + - openssl + run: + - python >=3.0 + - zlib + - bzip2 + - xz + - pigz + - htslib =1.8 + - matplotlib + - multiprocess + - samtools =1.8 + - gem3-mapper =gemBS_conda_v1 + - bs_call =2.02 + - ncurses + - curl + - openssl + +test: + commands: + - gemBS + +about: + home: https://github.com/heathsc/gemBS + license: GPL-3.0 + license_file: LICENSE.md + summary: gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS). + +extra: + identifiers: + - doi:10.1101/201988 From b582d12f0176e58b60c7d2d4dee01cc026262e37 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Mon, 23 Jul 2018 16:21:51 +0200 Subject: [PATCH 02/12] correcting dependencies --- recipes/gembs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml index 2d7e5d0238d8a..1ebef2116ffe5 100644 --- a/recipes/gembs/meta.yaml +++ b/recipes/gembs/meta.yaml @@ -27,10 +27,10 @@ requirements: - bzip2 - xz - htslib =1.8 - - ncurses - matplotlib - multiprocess - curl + - wget - openssl run: - python >=3.0 @@ -44,9 +44,9 @@ requirements: - samtools =1.8 - gem3-mapper =gemBS_conda_v1 - bs_call =2.02 - - ncurses - curl - openssl + - wget test: commands: From 3961356593b4c10d7d00659a0feab9ffcaf7c279 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Mon, 23 Jul 2018 15:52:04 +0200 Subject: [PATCH 03/12] gembs: passes a mulled build --- recipes/gem3-mapper/gemBS_conda_v1/build.sh | 12 ++++ recipes/gem3-mapper/gemBS_conda_v1/meta.yaml | 35 +++++++++++ recipes/gembs/build.sh | 6 ++ recipes/gembs/meta.yaml | 63 ++++++++++++++++++++ 4 files changed, 116 insertions(+) create mode 100644 recipes/gem3-mapper/gemBS_conda_v1/build.sh create mode 100644 recipes/gem3-mapper/gemBS_conda_v1/meta.yaml create mode 100644 recipes/gembs/build.sh create mode 100644 recipes/gembs/meta.yaml diff --git a/recipes/gem3-mapper/gemBS_conda_v1/build.sh b/recipes/gem3-mapper/gemBS_conda_v1/build.sh new file mode 100644 index 0000000000000..d325e176e8aa2 --- /dev/null +++ b/recipes/gem3-mapper/gemBS_conda_v1/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#adding include and library paths in order to find bzip2 +sed -i.bak ' + /^PATH_INCLUDE=/ s@$@ -I'$PREFIX'/include@ + /^PATH_LIB=/ s@$@ -L'$PREFIX'/lib@ + ' Makefile.mk.in + +./configure +make all +mkdir -p $PREFIX/bin +cp bin/* $PREFIX/bin diff --git a/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml b/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml new file mode 100644 index 0000000000000..c608f3a6ffc11 --- /dev/null +++ b/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "gemBS_conda_v1" %} +{% set sha256 = "3193250629bcf4567b832c5de3303e676d4a82bcdf84fecf24d2f7b2ab4398be" %} + +package: + name: gem3-mapper + version: {{ version }} + +source: + url: https://github.com/karl616/gem3-mapper/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - {{ compiler('c') }} + host: + - bzip2 + - zlib + run: + - bzip2 + - zlib + +test: + commands: + - gem-mapper 2>&1 | grep 'index|-I ' + - gem-indexer -h 2>&1 | grep 'input|-i (Multi-FASTA)' + - gem-retriever -h 2>&1 | grep 'index|-I (GEM archive)' + +about: + home: https://github.com/smarco/gem3-mapper + license: GPL3 + summary: The GEM read mapper (v3). + diff --git a/recipes/gembs/build.sh b/recipes/gembs/build.sh new file mode 100644 index 0000000000000..a078ced4005e2 --- /dev/null +++ b/recipes/gembs/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +#instead of installing software from submodules, let them be dependencies + +$PYTHON setup.py install --minimal + diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml new file mode 100644 index 0000000000000..2d7e5d0238d8a --- /dev/null +++ b/recipes/gembs/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "conda_v2" %} +{% set sha256 = "1ead3f20a36a40c0737ec58c2e783b9c1cb6a9de0317c0009964d1b164c598a0" %} +{% set bcftoolsversion = "1.8" %} +{% set bcftoolssha256 = "4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced"%} + +package: + name: gembs + version: {{ version }} + +source: + - url: https://github.com/karl616/gemBS/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + - url: https://github.com/samtools/bcftools/releases/download/{{ bcftoolsversion }}/bcftools-{{ bcftoolsversion }}.tar.bz2 + sha256: {{ bcftoolssha256 }} + folder: tools/bcftools + +build: + number: 0 + skip: True # [py27] + +requirements: + build: + - {{ compiler('c') }} + host: + - python >=3.0 + - zlib + - bzip2 + - xz + - htslib =1.8 + - ncurses + - matplotlib + - multiprocess + - curl + - openssl + run: + - python >=3.0 + - zlib + - bzip2 + - xz + - pigz + - htslib =1.8 + - matplotlib + - multiprocess + - samtools =1.8 + - gem3-mapper =gemBS_conda_v1 + - bs_call =2.02 + - ncurses + - curl + - openssl + +test: + commands: + - gemBS + +about: + home: https://github.com/heathsc/gemBS + license: GPL-3.0 + license_file: LICENSE.md + summary: gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS). + +extra: + identifiers: + - doi:10.1101/201988 From 046744dca45cd0426c8a2b5b6f7fd9bc16cde6c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Mon, 23 Jul 2018 16:21:51 +0200 Subject: [PATCH 04/12] correcting dependencies --- recipes/gembs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml index 2d7e5d0238d8a..1ebef2116ffe5 100644 --- a/recipes/gembs/meta.yaml +++ b/recipes/gembs/meta.yaml @@ -27,10 +27,10 @@ requirements: - bzip2 - xz - htslib =1.8 - - ncurses - matplotlib - multiprocess - curl + - wget - openssl run: - python >=3.0 @@ -44,9 +44,9 @@ requirements: - samtools =1.8 - gem3-mapper =gemBS_conda_v1 - bs_call =2.02 - - ncurses - curl - openssl + - wget test: commands: From e9e2fcff4fc35379e1bde90bc84234a53b70777f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Wed, 25 Jul 2018 18:50:37 +0200 Subject: [PATCH 05/12] pointing to the current gem3-mapper instead of a custom version --- recipes/gem3-mapper/gemBS_conda_v1/build.sh | 12 ------- recipes/gem3-mapper/gemBS_conda_v1/meta.yaml | 35 -------------------- recipes/gembs/build.sh | 2 +- recipes/gembs/meta.yaml | 2 +- 4 files changed, 2 insertions(+), 49 deletions(-) delete mode 100644 recipes/gem3-mapper/gemBS_conda_v1/build.sh delete mode 100644 recipes/gem3-mapper/gemBS_conda_v1/meta.yaml diff --git a/recipes/gem3-mapper/gemBS_conda_v1/build.sh b/recipes/gem3-mapper/gemBS_conda_v1/build.sh deleted file mode 100644 index d325e176e8aa2..0000000000000 --- a/recipes/gem3-mapper/gemBS_conda_v1/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/bash - -#adding include and library paths in order to find bzip2 -sed -i.bak ' - /^PATH_INCLUDE=/ s@$@ -I'$PREFIX'/include@ - /^PATH_LIB=/ s@$@ -L'$PREFIX'/lib@ - ' Makefile.mk.in - -./configure -make all -mkdir -p $PREFIX/bin -cp bin/* $PREFIX/bin diff --git a/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml b/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml deleted file mode 100644 index c608f3a6ffc11..0000000000000 --- a/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{% set version = "gemBS_conda_v1" %} -{% set sha256 = "3193250629bcf4567b832c5de3303e676d4a82bcdf84fecf24d2f7b2ab4398be" %} - -package: - name: gem3-mapper - version: {{ version }} - -source: - url: https://github.com/karl616/gem3-mapper/archive/{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 0 - -requirements: - build: - - {{ compiler('c') }} - host: - - bzip2 - - zlib - run: - - bzip2 - - zlib - -test: - commands: - - gem-mapper 2>&1 | grep 'index|-I ' - - gem-indexer -h 2>&1 | grep 'input|-i (Multi-FASTA)' - - gem-retriever -h 2>&1 | grep 'index|-I (GEM archive)' - -about: - home: https://github.com/smarco/gem3-mapper - license: GPL3 - summary: The GEM read mapper (v3). - diff --git a/recipes/gembs/build.sh b/recipes/gembs/build.sh index a078ced4005e2..73b16ce7bb839 100644 --- a/recipes/gembs/build.sh +++ b/recipes/gembs/build.sh @@ -2,5 +2,5 @@ #instead of installing software from submodules, let them be dependencies -$PYTHON setup.py install --minimal +$PYTHON setup.py install --minimal --single-version-externally-managed --record=record.txt diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml index 1ebef2116ffe5..ba12a49e9177e 100644 --- a/recipes/gembs/meta.yaml +++ b/recipes/gembs/meta.yaml @@ -42,7 +42,7 @@ requirements: - matplotlib - multiprocess - samtools =1.8 - - gem3-mapper =gemBS_conda_v1 + - gem3-mapper =3.6.1 - bs_call =2.02 - curl - openssl From f1e14b423ab825b7e8921afffde60c1fb6307106 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Fri, 27 Jul 2018 12:53:46 +0200 Subject: [PATCH 06/12] removing openssl --- recipes/gembs/meta.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml index ba12a49e9177e..481c8b3daa6f4 100644 --- a/recipes/gembs/meta.yaml +++ b/recipes/gembs/meta.yaml @@ -15,7 +15,7 @@ source: folder: tools/bcftools build: - number: 0 + number: 1 skip: True # [py27] requirements: @@ -31,7 +31,6 @@ requirements: - multiprocess - curl - wget - - openssl run: - python >=3.0 - zlib @@ -45,7 +44,6 @@ requirements: - gem3-mapper =3.6.1 - bs_call =2.02 - curl - - openssl - wget test: From e6208f2cb493fad249fdb37f236244ef9c3d140a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Mon, 23 Jul 2018 15:52:04 +0200 Subject: [PATCH 07/12] gembs: passes a mulled build --- recipes/gem3-mapper/gemBS_conda_v1/build.sh | 12 ++++ recipes/gem3-mapper/gemBS_conda_v1/meta.yaml | 35 +++++++++++ recipes/gembs/build.sh | 6 ++ recipes/gembs/meta.yaml | 63 ++++++++++++++++++++ 4 files changed, 116 insertions(+) create mode 100644 recipes/gem3-mapper/gemBS_conda_v1/build.sh create mode 100644 recipes/gem3-mapper/gemBS_conda_v1/meta.yaml create mode 100644 recipes/gembs/build.sh create mode 100644 recipes/gembs/meta.yaml diff --git a/recipes/gem3-mapper/gemBS_conda_v1/build.sh b/recipes/gem3-mapper/gemBS_conda_v1/build.sh new file mode 100644 index 0000000000000..d325e176e8aa2 --- /dev/null +++ b/recipes/gem3-mapper/gemBS_conda_v1/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +#adding include and library paths in order to find bzip2 +sed -i.bak ' + /^PATH_INCLUDE=/ s@$@ -I'$PREFIX'/include@ + /^PATH_LIB=/ s@$@ -L'$PREFIX'/lib@ + ' Makefile.mk.in + +./configure +make all +mkdir -p $PREFIX/bin +cp bin/* $PREFIX/bin diff --git a/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml b/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml new file mode 100644 index 0000000000000..c608f3a6ffc11 --- /dev/null +++ b/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "gemBS_conda_v1" %} +{% set sha256 = "3193250629bcf4567b832c5de3303e676d4a82bcdf84fecf24d2f7b2ab4398be" %} + +package: + name: gem3-mapper + version: {{ version }} + +source: + url: https://github.com/karl616/gem3-mapper/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - {{ compiler('c') }} + host: + - bzip2 + - zlib + run: + - bzip2 + - zlib + +test: + commands: + - gem-mapper 2>&1 | grep 'index|-I ' + - gem-indexer -h 2>&1 | grep 'input|-i (Multi-FASTA)' + - gem-retriever -h 2>&1 | grep 'index|-I (GEM archive)' + +about: + home: https://github.com/smarco/gem3-mapper + license: GPL3 + summary: The GEM read mapper (v3). + diff --git a/recipes/gembs/build.sh b/recipes/gembs/build.sh new file mode 100644 index 0000000000000..a078ced4005e2 --- /dev/null +++ b/recipes/gembs/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +#instead of installing software from submodules, let them be dependencies + +$PYTHON setup.py install --minimal + diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml new file mode 100644 index 0000000000000..2d7e5d0238d8a --- /dev/null +++ b/recipes/gembs/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "conda_v2" %} +{% set sha256 = "1ead3f20a36a40c0737ec58c2e783b9c1cb6a9de0317c0009964d1b164c598a0" %} +{% set bcftoolsversion = "1.8" %} +{% set bcftoolssha256 = "4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced"%} + +package: + name: gembs + version: {{ version }} + +source: + - url: https://github.com/karl616/gemBS/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + - url: https://github.com/samtools/bcftools/releases/download/{{ bcftoolsversion }}/bcftools-{{ bcftoolsversion }}.tar.bz2 + sha256: {{ bcftoolssha256 }} + folder: tools/bcftools + +build: + number: 0 + skip: True # [py27] + +requirements: + build: + - {{ compiler('c') }} + host: + - python >=3.0 + - zlib + - bzip2 + - xz + - htslib =1.8 + - ncurses + - matplotlib + - multiprocess + - curl + - openssl + run: + - python >=3.0 + - zlib + - bzip2 + - xz + - pigz + - htslib =1.8 + - matplotlib + - multiprocess + - samtools =1.8 + - gem3-mapper =gemBS_conda_v1 + - bs_call =2.02 + - ncurses + - curl + - openssl + +test: + commands: + - gemBS + +about: + home: https://github.com/heathsc/gemBS + license: GPL-3.0 + license_file: LICENSE.md + summary: gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS). + +extra: + identifiers: + - doi:10.1101/201988 From 491191b0f2d83a0506f2ba658c033d3a93a27cea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Mon, 23 Jul 2018 16:21:51 +0200 Subject: [PATCH 08/12] correcting dependencies --- recipes/gembs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml index 2d7e5d0238d8a..1ebef2116ffe5 100644 --- a/recipes/gembs/meta.yaml +++ b/recipes/gembs/meta.yaml @@ -27,10 +27,10 @@ requirements: - bzip2 - xz - htslib =1.8 - - ncurses - matplotlib - multiprocess - curl + - wget - openssl run: - python >=3.0 @@ -44,9 +44,9 @@ requirements: - samtools =1.8 - gem3-mapper =gemBS_conda_v1 - bs_call =2.02 - - ncurses - curl - openssl + - wget test: commands: From e5ab9ab248f8a2703cb1c3e5aa88fe16087a3336 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Wed, 25 Jul 2018 18:50:37 +0200 Subject: [PATCH 09/12] pointing to the current gem3-mapper instead of a custom version --- recipes/gem3-mapper/gemBS_conda_v1/build.sh | 12 ------- recipes/gem3-mapper/gemBS_conda_v1/meta.yaml | 35 -------------------- recipes/gembs/build.sh | 2 +- recipes/gembs/meta.yaml | 2 +- 4 files changed, 2 insertions(+), 49 deletions(-) delete mode 100644 recipes/gem3-mapper/gemBS_conda_v1/build.sh delete mode 100644 recipes/gem3-mapper/gemBS_conda_v1/meta.yaml diff --git a/recipes/gem3-mapper/gemBS_conda_v1/build.sh b/recipes/gem3-mapper/gemBS_conda_v1/build.sh deleted file mode 100644 index d325e176e8aa2..0000000000000 --- a/recipes/gem3-mapper/gemBS_conda_v1/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/bash - -#adding include and library paths in order to find bzip2 -sed -i.bak ' - /^PATH_INCLUDE=/ s@$@ -I'$PREFIX'/include@ - /^PATH_LIB=/ s@$@ -L'$PREFIX'/lib@ - ' Makefile.mk.in - -./configure -make all -mkdir -p $PREFIX/bin -cp bin/* $PREFIX/bin diff --git a/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml b/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml deleted file mode 100644 index c608f3a6ffc11..0000000000000 --- a/recipes/gem3-mapper/gemBS_conda_v1/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{% set version = "gemBS_conda_v1" %} -{% set sha256 = "3193250629bcf4567b832c5de3303e676d4a82bcdf84fecf24d2f7b2ab4398be" %} - -package: - name: gem3-mapper - version: {{ version }} - -source: - url: https://github.com/karl616/gem3-mapper/archive/{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 0 - -requirements: - build: - - {{ compiler('c') }} - host: - - bzip2 - - zlib - run: - - bzip2 - - zlib - -test: - commands: - - gem-mapper 2>&1 | grep 'index|-I ' - - gem-indexer -h 2>&1 | grep 'input|-i (Multi-FASTA)' - - gem-retriever -h 2>&1 | grep 'index|-I (GEM archive)' - -about: - home: https://github.com/smarco/gem3-mapper - license: GPL3 - summary: The GEM read mapper (v3). - diff --git a/recipes/gembs/build.sh b/recipes/gembs/build.sh index a078ced4005e2..73b16ce7bb839 100644 --- a/recipes/gembs/build.sh +++ b/recipes/gembs/build.sh @@ -2,5 +2,5 @@ #instead of installing software from submodules, let them be dependencies -$PYTHON setup.py install --minimal +$PYTHON setup.py install --minimal --single-version-externally-managed --record=record.txt diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml index 1ebef2116ffe5..ba12a49e9177e 100644 --- a/recipes/gembs/meta.yaml +++ b/recipes/gembs/meta.yaml @@ -42,7 +42,7 @@ requirements: - matplotlib - multiprocess - samtools =1.8 - - gem3-mapper =gemBS_conda_v1 + - gem3-mapper =3.6.1 - bs_call =2.02 - curl - openssl From 78f5a0b55f829eeab00195e0a64091af64378010 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Fri, 27 Jul 2018 12:53:46 +0200 Subject: [PATCH 10/12] removing openssl --- recipes/gembs/meta.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml index ba12a49e9177e..481c8b3daa6f4 100644 --- a/recipes/gembs/meta.yaml +++ b/recipes/gembs/meta.yaml @@ -15,7 +15,7 @@ source: folder: tools/bcftools build: - number: 0 + number: 1 skip: True # [py27] requirements: @@ -31,7 +31,6 @@ requirements: - multiprocess - curl - wget - - openssl run: - python >=3.0 - zlib @@ -45,7 +44,6 @@ requirements: - gem3-mapper =3.6.1 - bs_call =2.02 - curl - - openssl - wget test: From a2f31174d696aea40bbb88a6bcd9c8990f39c0c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Fri, 27 Jul 2018 13:08:17 +0200 Subject: [PATCH 11/12] starting build at 0 --- recipes/gembs/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml index 481c8b3daa6f4..b93991e928d9c 100644 --- a/recipes/gembs/meta.yaml +++ b/recipes/gembs/meta.yaml @@ -15,7 +15,7 @@ source: folder: tools/bcftools build: - number: 1 + number: 0 skip: True # [py27] requirements: From 00db44127e387a996cddf57ee92166fc50197cd2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karl=20Nordstr=C3=B6m?= Date: Fri, 27 Jul 2018 15:30:51 +0200 Subject: [PATCH 12/12] Changing to the main repository instead of the testing fork --- recipes/gembs/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml index 481c8b3daa6f4..1fbf21f1341ae 100644 --- a/recipes/gembs/meta.yaml +++ b/recipes/gembs/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "conda_v2" %} -{% set sha256 = "1ead3f20a36a40c0737ec58c2e783b9c1cb6a9de0317c0009964d1b164c598a0" %} +{% set version = "3.2.0" %} +{% set sha256 = "e3ee12740994cde0b94b932c5a23f9544951bde6d223aae4d0061876ef95a0c5" %} {% set bcftoolsversion = "1.8" %} {% set bcftoolssha256 = "4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced"%} @@ -8,15 +8,15 @@ package: version: {{ version }} source: - - url: https://github.com/karl616/gemBS/archive/{{ version }}.tar.gz + - url: https://github.com/heathsc/gemBS/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} - url: https://github.com/samtools/bcftools/releases/download/{{ bcftoolsversion }}/bcftools-{{ bcftoolsversion }}.tar.bz2 sha256: {{ bcftoolssha256 }} folder: tools/bcftools build: - number: 1 - skip: True # [py27] + number: 0 + skip: True # [py2k] requirements: build: