From 7f9a187e628138852d502d15fed9c73829a938d3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Wed, 12 Dec 2018 16:48:40 +0100 Subject: [PATCH 1/7] Bump spectra-cluster-cli --- recipes/spectra-cluster-cli/meta.yaml | 6 +++--- recipes/spectra-cluster-cli/spectra-cluster-cli.py | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/spectra-cluster-cli/meta.yaml b/recipes/spectra-cluster-cli/meta.yaml index 12a20cc279629..3e2166c0bb9b9 100644 --- a/recipes/spectra-cluster-cli/meta.yaml +++ b/recipes/spectra-cluster-cli/meta.yaml @@ -1,6 +1,6 @@ # Do not forget to update the version string in the peptide-shaker.py file -{% set version = "1.0.1" %} -{% set sha256 = "d83e5d47237f0c10cb68581941582e3e2fa630b079d68453a9b4b7397aeab49e" %} +{% set version = "1.1.2" %} +{% set sha256 = "978be823142a519fdfd79b9ea31a30385426f7935c3c94dc34aea94e85b5dd1e" %} package: name: spectra-cluster-cli @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 0 requirements: run: diff --git a/recipes/spectra-cluster-cli/spectra-cluster-cli.py b/recipes/spectra-cluster-cli/spectra-cluster-cli.py index a571b453d642c..f8dd104866906 100755 --- a/recipes/spectra-cluster-cli/spectra-cluster-cli.py +++ b/recipes/spectra-cluster-cli/spectra-cluster-cli.py @@ -12,7 +12,7 @@ from os import access from os import getenv from os import X_OK -jar_file = 'spectra-cluster-cli-1.0.1.jar' +jar_file = 'spectra-cluster-cli-1.1.2.jar' default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] From 8d0896caa6b90b28aa82a25eab111187a770c026 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Fri, 14 Dec 2018 13:34:51 +0100 Subject: [PATCH 2/7] Delete old pasta --- recipes/pasta/0.2/build.sh | 56 ---------------------------------- recipes/pasta/0.2/meta.yaml | 60 ------------------------------------- 2 files changed, 116 deletions(-) delete mode 100644 recipes/pasta/0.2/build.sh delete mode 100644 recipes/pasta/0.2/meta.yaml diff --git a/recipes/pasta/0.2/build.sh b/recipes/pasta/0.2/build.sh deleted file mode 100644 index 8135a4352b70f..0000000000000 --- a/recipes/pasta/0.2/build.sh +++ /dev/null @@ -1,56 +0,0 @@ -#!/bin/bash - -set -eu -o pipefail - -out_dir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -pasta_tools_dev_dir=$PREFIX/share -share_dir=$PREFIX/share - -mkdir -p $out_dir -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/pasta - -cp -R ./* $out_dir - -unamestr=`uname` -if [ $unamestr == 'Linux' ]; -then - wget --no-check-certificate https://github.com/smirarab/sate-tools-linux/archive/a3e6f56.tar.gz - tar -xzf a3e6f56.tar.gz - mv sate-tools-linux-a3e6f56372599ffacf1bd43adb2d67cf361228e2 sate-tools-linux - mv sate-tools-linux $pasta_tools_dev_dir - cd $out_dir - $PYTHON setup.py install - cp -R $share_dir/sate-tools-linux/* $PREFIX/bin -elif [ $unamestr == 'Darwin' ]; -then - export DYLD_LIBRARY_PATH=$PREFIX/lib - wget --no-check-certificate https://github.com/smirarab/sate-tools-mac/archive/0712214.tar.gz - tar -xzf 0712214.tar.gz - mv sate-tools-mac-0712214e20152b2ec989fc102602afa53d3a7b1a sate-tools-mac - mv sate-tools-mac $pasta_tools_dev_dir - cd $out_dir - $PYTHON setup.py install - cp -R $share_dir/sate-tools-mac/* $PREFIX/bin -fi - -# There seemes to be a bug in this version of Pasta. Executing the following -# with a valid input dataset: -# -# $python run_pasta.py -i input_fasta [-t starting_tree] -# -# produces the following error: -# -# PASTA ERROR: PASTA is exiting because of an error: -# '~/pasta/bin/hmmeralign' not found. Please install 'hmmeralign' and/or configure its location... -# -# Here is a work-around: -ln -s $PREFIX/bin/hmmalign $PREFIX/bin/hmmeralign -ln -s $PREFIX/bin/hmmbuild $PREFIX/bin/hmmerbuild - -cp $out_dir/pasta/*.py $PREFIX/pasta -cp $out_dir/run*.py $PREFIX - -# Allow for calling "pasta" from the command line. -ln -s $PREFIX/run_pasta.py $PREFIX/bin/pasta - diff --git a/recipes/pasta/0.2/meta.yaml b/recipes/pasta/0.2/meta.yaml deleted file mode 100644 index b295e24eb6215..0000000000000 --- a/recipes/pasta/0.2/meta.yaml +++ /dev/null @@ -1,60 +0,0 @@ -package: - name: pasta - version: "0.2" - -source: - url: https://github.com/smirarab/pasta/archive/6d52da1.tar.gz - md5: 69430d77b13f53505c3c9dc14bc1c4e2 - -build: - number: 1 - -requirements: - build: - - {{ compiler('c') }} - host: - - certifi - - dendropy <=3.13 - - gnu-wget - - java-jdk >=6 - - pcre - - python >=2.7,<3 - - pymongo - - setuptools - - run: - - dendropy <=3.13 - - java-jdk >=6 - - pcre - - python >=2.7,<3 - - pymongo - -test: - imports: - - pasta.alignment - - pasta.configure - - pasta.errors - - pasta.filemgr - - pasta.mainpasta - - pasta.pastaalignerjob - - pasta.pastajob - - pasta.scheduler - - pasta.settings - - pasta.tools - - pasta.treeholder - - pasta.tree - - pasta.usersettingclasses - - pasta.utility - commands: - - clustalw2 -help | grep OPTIONS - - hmmalign -h | grep HMMER - - hmmbuild -h | grep HMMER - - muscle -version | grep MUSCLE - - prank -help | grep prank - - raxml -h | grep raxmlHPC - - raxmlp -h | grep raxmlHPC - -about: - home: https://github.com/smirarab/pasta - license: GNU General Public License v3 or later (GPLv3+) - summary: 'An implementation of the PASTA (Practical Alignment using Sate and TrAnsitivity) algorithm' From 157a469d8fc7d9ec4da9082ca81435291d749707 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Fri, 14 Dec 2018 14:19:20 +0100 Subject: [PATCH 3/7] Rebuild pasta --- recipes/pasta/{1.7.8 => }/build.sh | 4 ++-- recipes/pasta/{1.7.8 => }/meta.yaml | 15 ++++++++------- 2 files changed, 10 insertions(+), 9 deletions(-) rename recipes/pasta/{1.7.8 => }/build.sh (90%) rename recipes/pasta/{1.7.8 => }/meta.yaml (84%) diff --git a/recipes/pasta/1.7.8/build.sh b/recipes/pasta/build.sh similarity index 90% rename from recipes/pasta/1.7.8/build.sh rename to recipes/pasta/build.sh index f60c427bbd681..3ef8da204e5fe 100644 --- a/recipes/pasta/1.7.8/build.sh +++ b/recipes/pasta/build.sh @@ -18,7 +18,7 @@ then tar -xzf a3e6f56.tar.gz mv sate-tools-linux-a3e6f56372599ffacf1bd43adb2d67cf361228e2 sate-tools-linux cd pasta - $PYTHON setup.py install + $PYTHON setup.py install --single-version-externally-managed --record=/tmp/record.txt mkdir $install_dir/sate-tools-linux cp -R $work_dir/sate-tools-linux/* $install_dir/sate-tools-linux/ # Handle a PASTA bug. @@ -33,7 +33,7 @@ then tar -xzf 0712214.tar.gz mv sate-tools-mac-0712214e20152b2ec989fc102602afa53d3a7b1a sate-tools-mac cd pasta - $PYTHON setup.py install + $PYTHON setup.py install --single-version-externally-managed --record=/tmp/record.txt mkdir $install_dir/sate-tools-mac cp -R $work_dir/sate-tools-mac/* $install_dir/sate-tools-mac/ # Handle a PASTA bug. diff --git a/recipes/pasta/1.7.8/meta.yaml b/recipes/pasta/meta.yaml similarity index 84% rename from recipes/pasta/1.7.8/meta.yaml rename to recipes/pasta/meta.yaml index ab4be78624071..b740885f4fa3d 100644 --- a/recipes/pasta/1.7.8/meta.yaml +++ b/recipes/pasta/meta.yaml @@ -4,28 +4,29 @@ package: source: url: https://github.com/smirarab/pasta/archive/43076b8.tar.gz - md5: a085bb4f6b4116566a61b785be580ae1 + sha256: 5eecec1710790df642696d1a52ecf723e5f02dd94e971427117344342a7c2a42 build: - number: 2 + number: 0 requirements: build: - {{ compiler('c') }} + host: - - certifi - - dendropy >=4.1.0 + - python + - setuptools + - dendropy >=4.4.0 - gnu-wget - java-jdk >=6 - pcre - - python - pymongo >=3.3.0 run: - - dendropy >=4.1.0 + - python + - dendropy >=4.4.0 - java-jdk >=6 - pcre - - python - pymongo >=3.3.0 test: From e3e8abab5f98af4a5bc415b2e35e52451a3effe7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Fri, 14 Dec 2018 14:20:36 +0100 Subject: [PATCH 4/7] Unblacklist pasta --- build-fail-blacklist | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 092143929463c..28ab2e21ad1c4 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1,3 +1,4 @@ + # The build string needs to be modified to account for the [nocairo] feature recipes/genometools-genometools/1.5.10-nocairo @@ -315,10 +316,6 @@ recipes/poretools/0.5.1 # RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://pypi.org/simple/pyaml/# recipes/hubward -# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://files.pythonhosted.org/packages/source/c/certifi/certifi-2016.9.26.tar.gz#md5=baa81e951a29958563689d868ef1064d -recipes/pasta/1.7.8 -recipes/pasta/0.2 - #failed to get install actions, retrying. exception was: The following specifications were found to be in conflict: # - numpy=1.9 # - qiime -> numpy=1.12 From 137783359ce1dba87b72ba957d0eae7c18e85550 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Fri, 14 Dec 2018 14:23:41 +0100 Subject: [PATCH 5/7] Revert dendropy version --- recipes/pasta/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pasta/meta.yaml b/recipes/pasta/meta.yaml index b740885f4fa3d..65fb45ea8b6d7 100644 --- a/recipes/pasta/meta.yaml +++ b/recipes/pasta/meta.yaml @@ -16,7 +16,7 @@ requirements: host: - python - setuptools - - dendropy >=4.4.0 + - dendropy >=4.1.0 - gnu-wget - java-jdk >=6 - pcre @@ -24,7 +24,7 @@ requirements: run: - python - - dendropy >=4.4.0 + - dendropy >=4.1.0 - java-jdk >=6 - pcre - pymongo >=3.3.0 From 8ed8234067963be76737710d0a73d7d3a312e70b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Fri, 14 Dec 2018 14:25:27 +0100 Subject: [PATCH 6/7] Correct build number --- recipes/pasta/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pasta/meta.yaml b/recipes/pasta/meta.yaml index 65fb45ea8b6d7..eba04fcb0260d 100644 --- a/recipes/pasta/meta.yaml +++ b/recipes/pasta/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 5eecec1710790df642696d1a52ecf723e5f02dd94e971427117344342a7c2a42 build: - number: 0 + number: 2 requirements: build: From 38194fb5ad3e5d7bb0a338fe2f7898d833cadcaf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Fri, 14 Dec 2018 14:35:36 +0100 Subject: [PATCH 7/7] Use openjdk --- recipes/pasta/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pasta/meta.yaml b/recipes/pasta/meta.yaml index eba04fcb0260d..695d989590da7 100644 --- a/recipes/pasta/meta.yaml +++ b/recipes/pasta/meta.yaml @@ -18,14 +18,14 @@ requirements: - setuptools - dendropy >=4.1.0 - gnu-wget - - java-jdk >=6 + - openjdk - pcre - pymongo >=3.3.0 run: - python - dendropy >=4.1.0 - - java-jdk >=6 + - openjdk - pcre - pymongo >=3.3.0