Update pinnings for bedtools (97 dependants) and bowtie2 (56 dependan…

…ts) (#13444) * Update pinnings for bedtools (97 dependants) and bowtie2 (56 dependants) * Update meta.yaml * fix checksum why oh why does this change ... * Try to speed up debugging of bowtie2 with new compilers * Update build.sh
bioconda · Feb 3, 2019 · d25cefc · d25cefc
1 parent 73c5e3c
commit d25cefc
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Showing 15 changed files with 22 additions and 33 deletions.
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -1,3 +1,6 @@
+recipes/bowtie2/2.2.1
+recipes/bowtie2/2.2.4
+recipes/bowtie2/2.2.5
 # The build string needs to be modified to account for the [nocairo] feature
 recipes/genometools-genometools/1.5.10-nocairo
 

diff --git a/recipes/bedtools/2.19.1/meta.yaml b/recipes/bedtools/2.19.1/meta.yaml
@@ -4,7 +4,7 @@ about:
   summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
 
 build:
-  number: 1
+  number: 2
 
 package:
   name: bedtools

diff --git a/recipes/bedtools/2.20.1/meta.yaml b/recipes/bedtools/2.20.1/meta.yaml
@@ -4,7 +4,7 @@ about:
   summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
 
 build:
-  number: 1
+  number: 2
 
 package:
   name: bedtools

diff --git a/recipes/bedtools/2.22/meta.yaml b/recipes/bedtools/2.22/meta.yaml
@@ -4,7 +4,7 @@ about:
   summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
 
 build:
-  number: 1
+  number: 2
 
 package:
   name: bedtools

diff --git a/recipes/bedtools/2.23.0/meta.yaml b/recipes/bedtools/2.23.0/meta.yaml
@@ -3,7 +3,7 @@ about:
   license: 'GPL v2'
   summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
 build:
-  number: 1
+  number: 2
 package:
   name: bedtools
   version: '2.23.0'

diff --git a/recipes/bedtools/2.25/meta.yaml b/recipes/bedtools/2.25/meta.yaml
@@ -7,7 +7,7 @@ source:
   sha256: d737ca42e7df76c5455d3e6e0562cdcb62336830eaad290fd4133a328a1ddacc
 
 build:
-  number: 4
+  number: 5
 
 requirements:
   build:

diff --git a/recipes/bedtools/2.26.0/meta.yaml b/recipes/bedtools/2.26.0/meta.yaml
@@ -9,7 +9,7 @@ source:
     - 2.26.0_postrelease.patch
 
 build:
-  number: 2
+  number: 3
 
 requirements:
   build:

diff --git a/recipes/bedtools/2.27.0/meta.yaml b/recipes/bedtools/2.27.0/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: e4f0e5616d04ba5ac09c36dec989b1236a5712e67d0b6874ff5e144d7ed4ce60
 
 build:
-  number: 2
+  number: 3
 
 requirements:
   build:

diff --git a/recipes/bedtools/2.27.1/meta.yaml b/recipes/bedtools/2.27.1/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: c8c2acbaf3f9cb92dcf8e5cd59af6b31ae9c4598efb786ba6c84f66ca72fafd9
 
 build:
-  number: 2
+  number: 3
 
 requirements:
   build:

diff --git a/recipes/bowtie2/2.2.1/meta.yaml b/recipes/bowtie2/2.2.1/meta.yaml
@@ -18,7 +18,7 @@ source:
   sha256: 32728b127abf0a8c3aa48e6fb8bf81a9133f54da7e065c2a7bd3410704195f9d
 
 build:
-  number: 0
+  number: 1
   skip: True  # [osx]
 
 requirements:

diff --git a/recipes/bowtie2/2.2.4/meta.yaml b/recipes/bowtie2/2.2.4/meta.yaml
@@ -15,10 +15,10 @@ package:
 
 source:
   url: https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.4/bowtie2-2.2.4-source.zip
-  md5sum: d41d8cd98f00b204e9800998ecf8427e # [linux]
+  md5: d31294875092e76ebb061eadc7998582
 
 build:
-  number: 2
+  number: 3
   skip: True  # [osx]
 
 requirements:

diff --git a/recipes/bowtie2/2.2.5/meta.yaml b/recipes/bowtie2/2.2.5/meta.yaml
@@ -20,7 +20,7 @@ source:
   sha256: 0f142477738accc73276f3e47877d54a64b6f7ac7911d0609b662adcd15374a0 # [osx]
 
 build:
-  number: 3
+  number: 4
 
 requirements:
   build:

diff --git a/recipes/bowtie2/bowtie2.patch b/recipes/bowtie2/bowtie2.patch
diff --git a/recipes/bowtie2/build.sh b/recipes/bowtie2/build.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 LDFLAGS=""
-make static-libs && make STATIC_BUILD=1
+make CXX=$CXX CPP=$CXX CC=$CC LDLIBS="-L$PREFIX/lib -lz -ltbb -ltbbmalloc -lpthread"
 
 binaries="\
 bowtie2 \

diff --git a/recipes/bowtie2/meta.yaml b/recipes/bowtie2/meta.yaml
@@ -8,20 +8,23 @@ package:
 source:
   url: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/{{ version }}/bowtie2-{{ version }}-source.zip
   sha256: 07ad2e1ce338ee461fb9559d6d21eacb10b16cfe2c973c2df08fbf0e33a9647a
-  patches:
-    - bowtie2.patch
 
 build:
-  number: 0
+  number: 1
 
 requirements:
   build:
     - {{ compiler('cxx') }}
   host:
     - python
+    - zlib
+    - tbb-devel
+    - tbb
   run:
     - python
     - perl
+    - zlib
+    - tbb
 
 test:
   commands: