From 096a148a3e64ba5da8df080e533e2ca8482c4777 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Fri, 1 Feb 2019 19:45:24 +0100 Subject: [PATCH 1/3] Bump deepTools and its dependencies --- recipes/bcftools/1.2/meta.yaml | 2 +- recipes/bcftools/1.3.1/meta.yaml | 2 +- recipes/bcftools/1.3/meta.yaml | 2 +- recipes/bcftools/meta.yaml | 2 +- recipes/deeptools/meta.yaml | 2 +- recipes/htslib/meta.yaml | 2 +- recipes/libdeflate/meta.yaml | 2 +- recipes/py2bit/meta.yaml | 2 +- recipes/pybigwig/0.1.11/meta.yaml | 2 +- recipes/pybigwig/meta.yaml | 2 +- recipes/pysam/0.10.0/meta.yaml | 2 +- recipes/pysam/0.7.7/meta.yaml | 2 +- recipes/pysam/0.8.3/meta.yaml | 2 +- recipes/pysam/0.9.1/meta.yaml | 2 +- recipes/pysam/meta.yaml | 2 +- recipes/samtools/1.6/meta.yaml | 2 +- recipes/samtools/meta.yaml | 2 +- 17 files changed, 17 insertions(+), 17 deletions(-) diff --git a/recipes/bcftools/1.2/meta.yaml b/recipes/bcftools/1.2/meta.yaml index e7a2a85cde390..a921049e2ce8d 100644 --- a/recipes/bcftools/1.2/meta.yaml +++ b/recipes/bcftools/1.2/meta.yaml @@ -2,7 +2,7 @@ package: name: bcftools version: "1.2" build: - number: 3 + number: 4 source: url: https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2 md5: 8044bed8fce62f7072fc6835420f0906 diff --git a/recipes/bcftools/1.3.1/meta.yaml b/recipes/bcftools/1.3.1/meta.yaml index 30d53b3bb06f0..fa4bbee170b8e 100644 --- a/recipes/bcftools/1.3.1/meta.yaml +++ b/recipes/bcftools/1.3.1/meta.yaml @@ -9,7 +9,7 @@ about: VCF and BCF and streams will work in most, but not all situations. build: - number: 3 + number: 4 package: name: bcftools diff --git a/recipes/bcftools/1.3/meta.yaml b/recipes/bcftools/1.3/meta.yaml index 57153ff34b87c..e7912b542f59d 100644 --- a/recipes/bcftools/1.3/meta.yaml +++ b/recipes/bcftools/1.3/meta.yaml @@ -8,7 +8,7 @@ test: - bcftools --version build: - number: 2 + number: 3 package: name: bcftools diff --git a/recipes/bcftools/meta.yaml b/recipes/bcftools/meta.yaml index 38eb80cfbbcf7..b301d73223432 100644 --- a/recipes/bcftools/meta.yaml +++ b/recipes/bcftools/meta.yaml @@ -10,7 +10,7 @@ about: VCF and BCF and streams will work in most, but not all situations. build: - number: 0 + number: 1 package: name: bcftools version: {{ version }} diff --git a/recipes/deeptools/meta.yaml b/recipes/deeptools/meta.yaml index 2e9a9387c1e9b..82ad9d47a69ac 100644 --- a/recipes/deeptools/meta.yaml +++ b/recipes/deeptools/meta.yaml @@ -7,7 +7,7 @@ source: sha256: bfbaf077d5206871f237fa4a8fd0da8ecf0d22f4e868fc6eeb215fd14574f3fb build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml index d668e7ec0a746..ecd34426ca70f 100644 --- a/recipes/htslib/meta.yaml +++ b/recipes/htslib/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2 diff --git a/recipes/libdeflate/meta.yaml b/recipes/libdeflate/meta.yaml index 4052bbaf5242b..604870843deda 100644 --- a/recipes/libdeflate/meta.yaml +++ b/recipes/libdeflate/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/py2bit/meta.yaml b/recipes/py2bit/meta.yaml index 55a60207c37f1..8cc141d9ff363 100644 --- a/recipes/py2bit/meta.yaml +++ b/recipes/py2bit/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.3.0" build: - number: 1 + number: 2 source: url: https://files.pythonhosted.org/packages/53/bb/547a927bed736ead3dc909e1e552d57c9034bb9493eff80544c0cf6e4828/py2bit-0.3.0.tar.gz diff --git a/recipes/pybigwig/0.1.11/meta.yaml b/recipes/pybigwig/0.1.11/meta.yaml index e38a43f7f07ee..b0826aa617ff5 100644 --- a/recipes/pybigwig/0.1.11/meta.yaml +++ b/recipes/pybigwig/0.1.11/meta.yaml @@ -8,7 +8,7 @@ source: sha256: 7b2d5897da5761b125e6a6efbaebe60ee81996546689ecd4b1493cc5ee14ae07 build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/pybigwig/meta.yaml b/recipes/pybigwig/meta.yaml index 58170ca5522e4..36c02ed968f2e 100644 --- a/recipes/pybigwig/meta.yaml +++ b/recipes/pybigwig/meta.yaml @@ -9,7 +9,7 @@ source: sha256: c65cb9ccd78a4ede00c3209579173e4f7e67598daf6dc079676a0e8982163f5b build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/pysam/0.10.0/meta.yaml b/recipes/pysam/0.10.0/meta.yaml index 5546c903d85c2..82ba934ce6b3f 100644 --- a/recipes/pysam/0.10.0/meta.yaml +++ b/recipes/pysam/0.10.0/meta.yaml @@ -9,7 +9,7 @@ source: - osx_rpath.patch [osx] build: - number: 6 + number: 7 skip: False binary_relocation: False # [linux] script: python -m pip install --no-deps --ignore-installed . diff --git a/recipes/pysam/0.7.7/meta.yaml b/recipes/pysam/0.7.7/meta.yaml index 34bcdd4980482..12fca279dfac3 100644 --- a/recipes/pysam/0.7.7/meta.yaml +++ b/recipes/pysam/0.7.7/meta.yaml @@ -7,7 +7,7 @@ source: sha256: c9f3018482eec99ee199dda3fdef2aa7424dde6574672a4c0d209a10985755cc build: - number: 2 + number: 3 skip: True # [not py27] requirements: diff --git a/recipes/pysam/0.8.3/meta.yaml b/recipes/pysam/0.8.3/meta.yaml index ec637d5fd99ff..0acb30114b9c7 100644 --- a/recipes/pysam/0.8.3/meta.yaml +++ b/recipes/pysam/0.8.3/meta.yaml @@ -7,7 +7,7 @@ source: md5: b1ae2a8ec3c6d20be30b2bc1aa995bbf build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/pysam/0.9.1/meta.yaml b/recipes/pysam/0.9.1/meta.yaml index 169c19990cdf2..8cd2d1b528a10 100644 --- a/recipes/pysam/0.9.1/meta.yaml +++ b/recipes/pysam/0.9.1/meta.yaml @@ -7,7 +7,7 @@ source: md5: d87765ad1e0afe534255c20cce5478e4 build: - number: 5 + number: 6 skip: False requirements: diff --git a/recipes/pysam/meta.yaml b/recipes/pysam/meta.yaml index 0def469a6ac15..e7ab33c8e3745 100644 --- a/recipes/pysam/meta.yaml +++ b/recipes/pysam/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 8cb3dd70f0d825086ac059ec2445ebd2ec5f14af73e7f1f4bd358966aaee5ed3 build: - number: 0 + number: 1 skip: False binary_relocation: False # [linux] diff --git a/recipes/samtools/1.6/meta.yaml b/recipes/samtools/1.6/meta.yaml index 3ff62883a7876..70f2483d04053 100644 --- a/recipes/samtools/1.6/meta.yaml +++ b/recipes/samtools/1.6/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index 8bfc3c204f679..dda98b5755603 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 From bedebdd9bc390364852e0abdc3e5dab2ac816cd5 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Fri, 1 Feb 2019 19:58:25 +0100 Subject: [PATCH 2/3] fix py2bit, remove obsolete pybigwig/0.1.11 --- recipes/py2bit/meta.yaml | 2 ++ recipes/pybigwig/0.1.11/build.sh | 10 ---------- recipes/pybigwig/0.1.11/meta.yaml | 29 ----------------------------- 3 files changed, 2 insertions(+), 39 deletions(-) delete mode 100644 recipes/pybigwig/0.1.11/build.sh delete mode 100644 recipes/pybigwig/0.1.11/meta.yaml diff --git a/recipes/py2bit/meta.yaml b/recipes/py2bit/meta.yaml index 8cc141d9ff363..cfe6a61234921 100644 --- a/recipes/py2bit/meta.yaml +++ b/recipes/py2bit/meta.yaml @@ -10,6 +10,8 @@ source: md5: 544a4bb602985d4026da0e01d96d2e3d requirements: + build: + - {{ compiler('c') }} host: - python - setuptools diff --git a/recipes/pybigwig/0.1.11/build.sh b/recipes/pybigwig/0.1.11/build.sh deleted file mode 100644 index 25fcd80549a81..0000000000000 --- a/recipes/pybigwig/0.1.11/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash - -export C_INCLUDE_PATH=$PREFIX/include -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/pybigwig/0.1.11/meta.yaml b/recipes/pybigwig/0.1.11/meta.yaml deleted file mode 100644 index b0826aa617ff5..0000000000000 --- a/recipes/pybigwig/0.1.11/meta.yaml +++ /dev/null @@ -1,29 +0,0 @@ -package: - name: pybigwig - version: '0.1.11' - -source: - #git_url: https://github.com/dpryan79/pyBigWig - url: https://github.com/dpryan79/pyBigWig/archive/0.1.11.tar.gz - sha256: 7b2d5897da5761b125e6a6efbaebe60ee81996546689ecd4b1493cc5ee14ae07 - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - python - - curl - run: - - python - - curl - - test: - imports: - - pyBigWig - -about: - home: https://github.com/dpryan79/pyBigWig - license: MIT - summary: A python extension written in C for quick access to bigWig files. From b81affc8e427e51ff9576604762b8e94b12e9138 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Fri, 1 Feb 2019 21:53:05 +0100 Subject: [PATCH 3/3] old pysam builds don't work with python 3.7 --- recipes/pysam/0.10.0/meta.yaml | 4 ++-- recipes/pysam/0.8.3/meta.yaml | 4 ++-- recipes/pysam/0.9.1/meta.yaml | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/pysam/0.10.0/meta.yaml b/recipes/pysam/0.10.0/meta.yaml index 82ba934ce6b3f..6ba68959c8457 100644 --- a/recipes/pysam/0.10.0/meta.yaml +++ b/recipes/pysam/0.10.0/meta.yaml @@ -22,7 +22,7 @@ requirements: - samtools >=1.3,<1.4 - bcftools >=1.3,<1.4 - cython - - python + - python <3.7 - pip - setuptools - zlib @@ -31,7 +31,7 @@ requirements: - htslib >=1.3,<1.4 - samtools >=1.3,<1.4 - bcftools >=1.3,<1.4 - - python + - python <3.7 - zlib - curl diff --git a/recipes/pysam/0.8.3/meta.yaml b/recipes/pysam/0.8.3/meta.yaml index 0acb30114b9c7..1c90c5dea21e8 100644 --- a/recipes/pysam/0.8.3/meta.yaml +++ b/recipes/pysam/0.8.3/meta.yaml @@ -13,12 +13,12 @@ requirements: build: - {{ compiler('c') }} host: - - python + - python <3.7 - setuptools - cython - zlib run: - - python + - python <3.7 - zlib test: diff --git a/recipes/pysam/0.9.1/meta.yaml b/recipes/pysam/0.9.1/meta.yaml index 8cd2d1b528a10..4c8d3a3a29715 100644 --- a/recipes/pysam/0.9.1/meta.yaml +++ b/recipes/pysam/0.9.1/meta.yaml @@ -18,7 +18,7 @@ requirements: - samtools ==1.3.1 - bcftools ==1.3.1 - cython - - python + - python <3.7 - setuptools - zlib - curl @@ -26,7 +26,7 @@ requirements: - htslib ==1.3.1 - samtools ==1.3.1 - bcftools ==1.3.1 - - python + - python <3.7 - zlib - curl