multiple fixes

bioconda · Jul 14, 2018 · 7f2d1f0 · 7f2d1f0
1 parent 99423c7
commit 7f2d1f0
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Showing 21 changed files with 64 additions and 19 deletions.
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -62,6 +62,7 @@ recipes/smalt
 recipes/trinity/2.1.1
 recipes/kaiju
 recipes/detonate
+recipes/minialign
 
 # needs some special treatment, shorter prefix than normal pkgs
 recipes/dimspy/1.1.0
@@ -77,6 +78,8 @@ recipes/fermikit
 # libxml2.so, not found
 recipes/dcmtk
 
+# build-error
+recipes/mimodd
 
 # The following recipes are also found in other channels (notably conda-forge).
 # They are placed here on the blacklist until we can deal with them further.
@@ -245,6 +248,7 @@ recipes/hmmer2
 # zlib
 recipes/hmmcopy
 recipes/haploclique/1.3.1
+recipes/migrate-n
 
 # CMake Error: The source directory "/opt/conda/conda-bld/sqlitebrowser_1529759350498/work" does not appear to contain CMakeLists.txt.
 recipes/sqlitebrowser
@@ -1537,7 +1541,10 @@ recipes/bioconductor-zlibbioc
 # unknown
 recipes/smina
 # missing tarball
+recipes/metagene_annotator
 recipes/sloika
+
+
 # missing dep
 recipes/sistr_cmd
 # missing file
@@ -1578,6 +1585,7 @@ recipes/repeatmasker
 
 # zlib missing
 recipes/rascaf
+recipes/merlin
 
 #RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/click/
 recipes/query_phenomizer
@@ -1617,6 +1625,14 @@ recipes/bamm
 recipes/bcftools/1.2
 recipes/bcftools/1.3
 recipes/ema
+recipes/lordec
+recipes/libssw
+
+# aclocal error, but also downloads mauve tarballs, but there is now a mauve pkgs, is it still needed?
+recipes/libmuscle
+
+# compilation error
+recipes/libsbml
 
 # unable to access jarfile
 recipes/effectivet3
@@ -1955,6 +1971,12 @@ recipes/antarna
 
 # missing gfortran
 recipes/tepid
+recipes/ig-checkflowtypes
+recipes/epicseg
+
+
+#gff.h missing
+recipes/gffcompare
 
 # perl errors
 recipes/snvphyl-tools
@@ -2285,6 +2307,7 @@ recipes/hurry.filesize
 
 # missing tarball
 recipes/knot
+recipes/moreutils
 
 # compilation error, missing boost header
 recipes/k-slam
@@ -2309,3 +2332,7 @@ recipes/fastspar
 
 # build error
 recipes/mapsplice
+
+# no target specified and no make file
+recipes/mreps
+
diff --git a/recipes/express/meta.yaml b/recipes/express/meta.yaml
@@ -14,6 +14,8 @@ source:
 requirements:
   build:
     - {{ compiler('cxx') }}
+  run:
+    - zlib
 
 test:
   commands:

diff --git a/recipes/flexbar/2.5.0/meta.yaml b/recipes/flexbar/2.5.0/meta.yaml
@@ -15,7 +15,7 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
     - cmake
   host:
     - tbb

diff --git a/recipes/libbambamc/0.5.00/meta.yaml b/recipes/libbambamc/0.5.00/meta.yaml
@@ -13,6 +13,7 @@ build:
 requirements:
   build:
     - {{ compiler('c') }}
+  host:
     - zlib
   run:
     - zlib

diff --git a/recipes/libmuscle/meta.yaml b/recipes/libmuscle/meta.yaml
@@ -14,11 +14,11 @@ source:
 
 requirements:
   build:
-  - {{ compiler('c') }}
-  - autoconf
-  - automake
-  - perl
-  - libtool
+    - {{ compiler('c') }}
+    - autoconf
+    - automake
+    - perl
+    - libtool
 
   run:
 

diff --git a/recipes/lightning/meta.yaml b/recipes/lightning/meta.yaml
@@ -3,7 +3,7 @@ package:
   version: '0.2.dev0'
 
 source:
-  url: https://github.com/scikit-learn-contrib/lightning/tarball/3eb7155
+  url: https://github.com/scikit-learn-contrib/lightning/archive/3eb71555186ffff1a809e923ddc487e4cc37332f.tar.gz
   md5: ca950c86f9a54e8f681e8cbd36a82f13
 
 build:
@@ -16,7 +16,6 @@ requirements:
     - scikit-learn
     - numpy
     - scipy
-
   run:
     - python
     - scikit-learn

diff --git a/recipes/ls-gkm/meta.yaml b/recipes/ls-gkm/meta.yaml
@@ -13,7 +13,7 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
 
   run:
 

diff --git a/recipes/manorm/meta.yaml b/recipes/manorm/meta.yaml
@@ -39,3 +39,8 @@ about:
   license_family: BSD
   license_file: LICENSE
   summary: A robust model for quantitative comparison of ChIP-Seq data sets.
+
+extra:
+  container:
+    # needs libGL.so.1
+    extended-base: true
diff --git a/recipes/mashmap/meta.yaml b/recipes/mashmap/meta.yaml
@@ -14,7 +14,7 @@ source:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
     - autoconf
     - automake
     - m4

diff --git a/recipes/mentalist/meta.yaml b/recipes/mentalist/meta.yaml
@@ -14,7 +14,7 @@ build:
   skip: True  # [osx]
 
 requirements:
-  build:
+  run:
     - julia 0.6.1
     - hdf5
     - mpfr

diff --git a/recipes/metfrag/meta.yaml b/recipes/metfrag/meta.yaml
@@ -9,7 +9,7 @@ package:
 
 source:
   url: http://msbi.ipb-halle.de/~cruttkie/metfrag/MetFrag2.4.5-CL.jar
-  sha256: fa66a79e9394d7cbe22e55e10d2e15e0b0457e4b3636f1f4e37bc02ae9c868bb
+  sha256: 7d05cb5d7e72872b6ed13495811f1eb9155943ff9f8903cb4240c6f379731174
 
 build:
   number: 3

diff --git a/recipes/methyldackel/build.sh b/recipes/methyldackel/build.sh
@@ -1,4 +1,13 @@
 #!/bin/bash
+
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LD_LIBRARY_PATH="${PREFIX}/lib"
+
+export LDFLAGS="-L${PREFIX}/lib"
+export CPPFLAGS="-I${PREFIX}/include"
+export CFLAGS="-I${PREFIX}/include"
+
 export C_INCLUDE_PATH=$PREFIX/include
 make
 make install prefix=$PREFIX/bin
diff --git a/recipes/micro_razers/meta.yaml b/recipes/micro_razers/meta.yaml
@@ -12,7 +12,7 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
     - cmake
   host:
     - zlib

diff --git a/recipes/mlrho/meta.yaml b/recipes/mlrho/meta.yaml
@@ -15,6 +15,7 @@ source:
 requirements:
   build:
     - {{ compiler('c') }}
+  host:
     - gsl
   run:
     - gsl

diff --git a/recipes/mmseqs2/meta.yaml b/recipes/mmseqs2/meta.yaml
@@ -14,7 +14,7 @@ source:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
     - cmake
     - make
   host:

diff --git a/recipes/mosaik/meta.yaml b/recipes/mosaik/meta.yaml
@@ -16,7 +16,7 @@ source:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
   host:
     - zlib
   run:

diff --git a/recipes/mreps/meta.yaml b/recipes/mreps/meta.yaml
@@ -11,7 +11,7 @@ source:
 
 requirements:
   build:
-  - {{ compiler('c') }}
+    - {{ compiler('c') }}
 
   run:
 

diff --git a/recipes/ms/meta.yaml b/recipes/ms/meta.yaml
@@ -14,7 +14,7 @@ requirements:
 
 source:
   url: https://webshare.uchicago.edu/users/rhudson1/Public/ms.folder/ms.tar.gz
-  md5: ef693dcc424fd5293b0bea4c68953700
+  md5: fb28b4dac40a233dba9e7a661906ecf7
 
 test:
   commands:

diff --git a/recipes/openms/2.2.0/meta.yaml b/recipes/openms/2.2.0/meta.yaml
@@ -15,7 +15,7 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
     - cmake
   host:
     - glib

diff --git a/recipes/openms/2.3.0/meta.yaml b/recipes/openms/2.3.0/meta.yaml
@@ -16,7 +16,7 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
     - cmake
     - autoconf
     - automake

diff --git a/recipes/osra/2.0.1/meta.yaml b/recipes/osra/2.0.1/meta.yaml
@@ -17,6 +17,7 @@ requirements:
   host:
     - openbabel ==2.4.1
     - graphicsmagick ==1.3.23
+    - perl
     - tesseract
     - potrace
     - tclap
-Original file line number
+Diff line change
@@ Expand Up / @@ -14,6 +14,8 @@ source: @@
     requirements:
       build:
         - {{ compiler('cxx') }}
+      run:
+        - zlib
     test:
       commands:
@@ Expand Down @@