Blacklist update (#18992)

* Blacklist update * update recipes * maybe antismash will work now * Update build.sh
bioconda · Nov 29, 2019 · 2cd2f29 · 2cd2f29
1 parent 87dd993
commit 2cd2f29
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Showing 9 changed files with 18 additions and 21 deletions.
diff --git 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
@@ -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
@@ -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
@@ -1,4 +1,4 @@
 #!/bin/bash
 
 # download the databases required by several options
-$PREFIX/bin/download-antismash-databases
+download-antismash-databases
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
Original file line number	Diff line number	Diff line change
Expand Up		@@ -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
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,6 +18,7 @@ requirements: @@
         - cwltool
         - dxpy
         - pyyaml
+        - futures
     test:
       commands:
@@ Expand Down @@