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Update pinnings for bedtools (97 dependants) and bowtie2 (56 dependants) #13444

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merged 5 commits into from
Feb 3, 2019
Merged

Update pinnings for bedtools (97 dependants) and bowtie2 (56 dependants) #13444

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90a4d04
Update pinnings for bedtools (97 dependants) and bowtie2 (56 dependants)
dpryan79 Feb 2, 2019
2231cf7
Update meta.yaml
dpryan79 Feb 2, 2019
6d82118
fix checksum
bgruening Feb 2, 2019
274f4aa
Try to speed up debugging of bowtie2 with new compilers
dpryan79 Feb 3, 2019
8f201e1
Update build.sh
dpryan79 Feb 3, 2019
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3 changes: 3 additions & 0 deletions build-fail-blacklist
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Original file line number Diff line number Diff line change
@@ -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

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2 changes: 1 addition & 1 deletion recipes/bedtools/2.19.1/meta.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion recipes/bedtools/2.20.1/meta.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion recipes/bedtools/2.22/meta.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion recipes/bedtools/2.23.0/meta.yaml
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Expand Up @@ -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'
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2 changes: 1 addition & 1 deletion recipes/bedtools/2.25/meta.yaml
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Expand Up @@ -7,7 +7,7 @@ source:
sha256: d737ca42e7df76c5455d3e6e0562cdcb62336830eaad290fd4133a328a1ddacc

build:
number: 4
number: 5

requirements:
build:
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2 changes: 1 addition & 1 deletion recipes/bedtools/2.26.0/meta.yaml
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Expand Up @@ -9,7 +9,7 @@ source:
- 2.26.0_postrelease.patch

build:
number: 2
number: 3

requirements:
build:
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2 changes: 1 addition & 1 deletion recipes/bedtools/2.27.0/meta.yaml
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Expand Up @@ -10,7 +10,7 @@ source:
sha256: e4f0e5616d04ba5ac09c36dec989b1236a5712e67d0b6874ff5e144d7ed4ce60

build:
number: 2
number: 3

requirements:
build:
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2 changes: 1 addition & 1 deletion recipes/bedtools/2.27.1/meta.yaml
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Expand Up @@ -10,7 +10,7 @@ source:
sha256: c8c2acbaf3f9cb92dcf8e5cd59af6b31ae9c4598efb786ba6c84f66ca72fafd9

build:
number: 2
number: 3

requirements:
build:
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2 changes: 1 addition & 1 deletion recipes/bowtie2/2.2.1/meta.yaml
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Expand Up @@ -18,7 +18,7 @@ source:
sha256: 32728b127abf0a8c3aa48e6fb8bf81a9133f54da7e065c2a7bd3410704195f9d

build:
number: 0
number: 1
skip: True # [osx]

requirements:
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4 changes: 2 additions & 2 deletions recipes/bowtie2/2.2.4/meta.yaml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion recipes/bowtie2/2.2.5/meta.yaml
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Expand Up @@ -20,7 +20,7 @@ source:
sha256: 0f142477738accc73276f3e47877d54a64b6f7ac7911d0609b662adcd15374a0 # [osx]

build:
number: 3
number: 4

requirements:
build:
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17 changes: 0 additions & 17 deletions recipes/bowtie2/bowtie2.patch
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This file was deleted.

2 changes: 1 addition & 1 deletion recipes/bowtie2/build.sh
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@@ -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 \
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9 changes: 6 additions & 3 deletions recipes/bowtie2/meta.yaml
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Expand Up @@ -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:
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