From 2cd2f29bb28c84f13b572b9007a55983d2392ed5 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Fri, 29 Nov 2019 19:54:30 +0100 Subject: [PATCH] Blacklist update (#18992) * Blacklist update * update recipes * maybe antismash will work now * Update build.sh --- build-fail-blacklist | 5 ----- recipes/antismash/build.sh | 2 +- recipes/antismash/meta.yaml | 2 ++ recipes/antismash/post-link.sh | 2 +- recipes/dx-cwl/meta.yaml | 1 + recipes/fastqmetrics/meta.yaml | 2 +- recipes/maxentscan/meta.yaml | 2 +- recipes/theta2/build.sh | 6 +++--- recipes/theta2/meta.yaml | 17 ++++++++--------- 9 files changed, 18 insertions(+), 21 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 7aed4fe3c9d63..5e826518868fe 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -41,11 +41,6 @@ recipes/pbbam recipes/bmtagger # Packages failing in bulk that haven't yet received more attention -recipes/dx-cwl -recipes/theta2 -recipes/maxentscan -recipes/antismash -recipes/fastqmetrics recipes/qiimetomaaslin recipes/glimmerhmm recipes/python-omero diff --git a/recipes/antismash/build.sh b/recipes/antismash/build.sh index b5afa4a91a4ea..c1a4310ffd2b9 100644 --- a/recipes/antismash/build.sh +++ b/recipes/antismash/build.sh @@ -2,4 +2,4 @@ echo "include antismash/generic_modules/genefinding/train_crypto" >> MANIFEST.in -$PYTHON setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/antismash/meta.yaml b/recipes/antismash/meta.yaml index 973e7fc3ed176..9e6a349bbcd86 100644 --- a/recipes/antismash/meta.yaml +++ b/recipes/antismash/meta.yaml @@ -21,6 +21,8 @@ requirements: - python >=2.7,<3.0a0 - pip - icu + - backports.lzma + - hmmer ==3.1b2 run: - python >=2.7,<3.0a0 - argparse diff --git a/recipes/antismash/post-link.sh b/recipes/antismash/post-link.sh index 48d76eac314e0..26fdad9e1d1cd 100644 --- a/recipes/antismash/post-link.sh +++ b/recipes/antismash/post-link.sh @@ -1,4 +1,4 @@ #!/bin/bash # download the databases required by several options -$PREFIX/bin/download-antismash-databases \ No newline at end of file +download-antismash-databases diff --git a/recipes/dx-cwl/meta.yaml b/recipes/dx-cwl/meta.yaml index 8b08f4bb66d6b..42bf9d1a47946 100644 --- a/recipes/dx-cwl/meta.yaml +++ b/recipes/dx-cwl/meta.yaml @@ -18,6 +18,7 @@ requirements: - cwltool - dxpy - pyyaml + - futures test: commands: diff --git a/recipes/fastqmetrics/meta.yaml b/recipes/fastqmetrics/meta.yaml index e9b7200966252..8e987a14b1b6a 100644 --- a/recipes/fastqmetrics/meta.yaml +++ b/recipes/fastqmetrics/meta.yaml @@ -21,7 +21,7 @@ requirements: - pip run: - python >=3 - - nanoget >=0.14.0 + - nanoget >=0.14.0,<1.8.0 test: imports: diff --git a/recipes/maxentscan/meta.yaml b/recipes/maxentscan/meta.yaml index bd1aea2af8bab..99be02886a197 100644 --- a/recipes/maxentscan/meta.yaml +++ b/recipes/maxentscan/meta.yaml @@ -2,7 +2,7 @@ package: name: maxentscan version: "0_2004.04.21" source: - url: http://genes.mit.edu/burgelab/maxent/download/fordownload.tar.gz + url: http://hollywood.mit.edu/burgelab/maxent/download/fordownload.tar.gz md5: 6f1fabda518998bf8c001149c9cb3b5f build: diff --git a/recipes/theta2/build.sh b/recipes/theta2/build.sh index ca47e6c48aeda..38d80f7c58b4a 100644 --- a/recipes/theta2/build.sh +++ b/recipes/theta2/build.sh @@ -4,14 +4,14 @@ set -eu outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $outdir mkdir -p $PREFIX/bin -cp -r python $outdir +cp python/* $outdir # bnpy dependency wget -O bnpy-dev.zip https://bitbucket.org/michaelchughes/bnpy-dev/get/590663f97f93.zip unzip bnpy-dev.zip -mv michaelchughes-bnpy-dev-590663f97f93/bnpy $outdir/python +mv michaelchughes-bnpy-dev-590663f97f93/bnpy $outdir -maincmd=$outdir/python/RunTHetA.py +maincmd=$outdir/RunTHetA.py sed -i.bak '1i#!/opt/anaconda1anaconda2anaconda3/bin/python' $maincmd sed -i.bak '2iimport os\nthis_dir = os.path.realpath(os.path.join(os.getcwd(), os.path.dirname(os.path.realpath(__file__))))\nimport sys\nsys.path.append(this_dir)' $maincmd chmod a+x $maincmd diff --git a/recipes/theta2/meta.yaml b/recipes/theta2/meta.yaml index f800fd4c51bd8..b081405b5a7b9 100644 --- a/recipes/theta2/meta.yaml +++ b/recipes/theta2/meta.yaml @@ -1,21 +1,19 @@ +{% set version = "0.7" %} + package: name: theta2 - version: '0.7' + version: {{ version }} + build: number: 2 - noarch: python + noarch: generic + source: - url: https://github.com/raphael-group/THetA/archive/v0.7.tar.gz + url: https://github.com/raphael-group/THetA/archive/v{{ version }}.tar.gz sha256: 474452fa87a1ca0228137693bfede3200b91e4e166b2216c4bd24f8b270c1dea requirements: host: - - python <3 - - numpy - - scipy - - matplotlib - - joblib - - numexpr - wget - unzip run: @@ -33,4 +31,5 @@ test: about: home: https://github.com/raphael-group/THetA license: Modified MIT (no inclusion in commercial tools) + license_file: README.txt summary: Estimate tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data