Merge branch 'master' of https://github.com/bioconda/bioconda-recipes

StevenVerbruggen · Mar 9, 2018 · 097d03e · 097d03e
2 parents c9a1371 + 6f320c2
commit 097d03e
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -20,7 +20,6 @@ recipes/frc
 recipes/r-pscbs/0.61.0
 
 # ERROR: cannot verify github.com's certificate, issued by ‘CN=DigiCert SHA2 Extended Validation Server CA,OU=www.digicert.com,O=DigiCert Inc,C=US’:
-recipes/ngless
 recipes/transrate-tools
 
 recipes/openslide

diff --git a/recipes/ficus/build.sh b/recipes/ficus/build.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-$PYTHON setup.py install
+$PYTHON setup.py install --single-version-externally-managed --record=record.txt
 
 # Add more build steps here, if they are necessary.
 

diff --git a/recipes/ficus/meta.yaml b/recipes/ficus/meta.yaml
@@ -1,26 +1,27 @@
+{% set version = "0.5" %}
+
 package:
   name: ficus
-  version: "0.3"
+  version: {{ version }}
 
 source:
-  fn: ficus-0.3.tar.gz
-  url: https://pypi.python.org/packages/1a/ec/b92090badf7093ab2a329f2be6e7ded0803f7dfe0b8196bc3881a53b19b2/ficus-0.3.tar.gz
-  md5: 979a9b00e2241d3dbc77687bda1a1859 
+  fn: ficus-{{ version }}.tar.gz
+  url: https://github.com/camillescott/ficus/archive/v{{ version }}.tar.gz
+  sha256: 9019a9a6d2eb7de5afa0e6ab3f6d56f1258560402f6c9c5301f7e44665903d3b
 
 build:
-  skip: True # [not py27]
   number: 0
 
 requirements:
   build:
     - python
-    - matplotlib
-    - nose-capturestderr
+    - matplotlib >=1.4
+    - pytest
+    - pytest-runner
 
   run:
     - python
-    - matplotlib
-    - nose-capturestderr
+    - matplotlib >=1.4
 
 test:
   # Python imports
@@ -29,5 +30,5 @@ test:
 
 about:
   home: https://github.com/camillescott/ficus
-  license: BSD
-  summary: Ficus provides a context manager for matplotlib figures. 
+  license: BSD-3-Clause
+  summary: provides a context manager for matplotlib figures. 
diff --git a/recipes/mqc/meta.yaml b/recipes/mqc/meta.yaml
@@ -8,7 +8,7 @@ source:
 
 build:
   skip: True  # [not py27]
-  number: 0
+  number: 1
 
 requirements:
   run:
@@ -23,13 +23,14 @@ requirements:
     - perl-dbi
     - perl-dbd-sqlite
     - perl-parallel-forkmanager
-    - plastid
+    - plastid 0.4.7 py27_0
     - samtools
     - pysam 0.11*
 
 test:
   commands:
     - mQC.pl --help
+    - psite -h
 
 about:
   home: https://github.com/Biobix/mQC

diff --git a/recipes/ngless/build.sh b/recipes/ngless/build.sh
@@ -6,14 +6,12 @@ export CPPFLAGS="-I${PREFIX}/include"
 export CFLAGS="-I$PREFIX/include"
 export CPATH=${PREFIX}/include
 
-# internal download failes with:
-# ERROR: cannot verify github.com's certificate, issued by ‘CN=DigiCert SHA2 Extended Validation Server CA,OU=www.digicert.com,O=DigiCert Inc,C=US’:
-# Unable to locally verify the issuer's authority.
-#
-alias wget='wget --no-check-certificate'
 
-stack setup
-stack update
+# stack relies on $HOME, so fake it:
+mkdir -p fake-home
+export HOME=$PWD/fake-home
+export STACK_ROOT="$HOME/.stack"
+stack setup --local-bin-path ${PREFIX}/bin
 make install prefix=$PREFIX
 
 #cleanup

diff --git a/recipes/ngless/meta.yaml b/recipes/ngless/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ngless" %}
-{% set version = "0.6.1" %}
-{% set md5 = "9e7657eee1af7da092255c43873c19da" %}
+{% set version = "0.7.0" %}
+{% set md5 = "abce9861f978cedbc528e00a3b5b8d2c" %}
 
 package:
   name: {{ name }}
@@ -10,14 +10,18 @@ source:
   fn: {{ version }}.tar.gz
   url: https://github.com/luispedro/ngless/archive/v{{ version }}.tar.gz
   md5: {{ md5 }}
+  patches:
+   - use_lts_9_21.patch
+   - remove_inline_cpp.patch
+   - wget-no-check-certificat.patch
 
 build:
-  number: 1
+  number: 0
   skip: True  #  [osx]
 
 requirements:
   build:
-    - stack >=1.3.2
+    - stack >=1.6.5
     - bzip2 {{ CONDA_BZIP2 }}*
     - gmp {{CONDA_GMP}}*
     - zlib {{CONDA_ZLIB}}*