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bump zlib requirement to be in sync with conda-forge #7385

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merged 11 commits into from
Feb 3, 2018
Merged

bump zlib requirement to be in sync with conda-forge #7385

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219d961
bump versoin number for new zlib version, add zlib ENV var
bgruening Jan 27, 2018
895511c
increase zlib dependency
bgruening Jan 27, 2018
3001cc1
pin zlib in ucsc template
bgruening Jan 27, 2018
1c6aba7
add missing htslib pinning
bgruening Feb 3, 2018
278f119
incease htslib version
bgruening Feb 3, 2018
4670651
increase build number
bgruening Feb 3, 2018
dff78cd
fix review comments
bgruening Feb 3, 2018
33d8ab3
a few more review comment fixes
bgruening Feb 3, 2018
28e8c2c
next round of fixes
bgruening Feb 3, 2018
56d2d51
last lint fixes
bgruening Feb 3, 2018
fc0e434
wub: no need for rebuild
mbargull Feb 3, 2018
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24 changes: 12 additions & 12 deletions recipes/abricate/0.4/meta.yaml
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Expand Up @@ -3,7 +3,7 @@ package:
version: "0.4"

build:
number: 0
number: 1

source:
fn: abricate_v0.4.tar.gz
Expand All @@ -12,18 +12,18 @@ source:

requirements:
build:
- gcc # [linux]
- llvm # [osx]
- zlib
- gcc # [linux]
- llvm # [osx]
- zlib {{CONDA_ZLIB}}*
run:
- libgcc # [linux]
- perl
- perl-bioperl >=1.6.924
- perl-file-slurp
- perl-text-csv
- perl-list-moreutils
- blast >=2.2.30
- zlib
- libgcc # [linux]
- perl
- perl-bioperl >=1.6.924
- perl-file-slurp
- perl-text-csv
- perl-list-moreutils
- blast >=2.2.30
- zlib {{CONDA_ZLIB}}*

test:
commands:
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50 changes: 25 additions & 25 deletions recipes/abricate/0.5/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,35 +1,35 @@
package:
name: abricate
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4-space indentation

version: "0.5"
name: abricate
version: "0.5"

build:
number: 0
number: 1

source:
fn: abricate_v0.5.tar.gz
url: https://github.com/tseemann/abricate/archive/v0.5.tar.gz
md5: 9d2b54511190c3beb6e018675c4d4d0e
fn: abricate_v0.5.tar.gz
url: https://github.com/tseemann/abricate/archive/v0.5.tar.gz
md5: 9d2b54511190c3beb6e018675c4d4d0e

requirements:
build:
- gcc # [linux]
- llvm # [osx]
- zlib
run:
- libgcc # [linux]
- perl
- perl-bioperl >=1.6.924
- perl-file-slurp
- perl-text-csv
- perl-list-moreutils
- perl-file-spec
- perl-json
- perl-lwp-simple
- perl-findbin
- blast >=2.2.30
- zlib
- unzip
- emboss
build:
- gcc # [linux]
- llvm # [osx]
- zlib {{CONDA_ZLIB}}*
run:
- libgcc # [linux]
- perl
- perl-bioperl >=1.6.924
- perl-file-slurp
- perl-text-csv
- perl-list-moreutils
- perl-file-spec
- perl-json
- perl-lwp-simple
- perl-findbin
- blast >=2.2.30
- zlib {{CONDA_ZLIB}}*
- unzip
- emboss

test:
commands:
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58 changes: 29 additions & 29 deletions recipes/abricate/meta.yaml
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Expand Up @@ -3,7 +3,7 @@ package:
version: "0.7"

build:
number: 0
number: 1

source:
fn: abricate_v0.7.tar.gz
Expand All @@ -12,35 +12,35 @@ source:

requirements:
build:
- gcc # [linux]
- llvm # [osx]
- zlib
- perl
- perl-bioperl >=1.6.924
- perl-file-slurp
- perl-text-csv
- perl-list-moreutils
- perl-file-spec
- perl-json
- perl-lwp-simple
- perl-findbin
- blast >=2.6
- gcc # [linux]
- llvm # [osx]
- zlib {{CONDA_ZLIB}}*
- perl
- perl-bioperl >=1.6.924
- perl-file-slurp
- perl-text-csv
- perl-list-moreutils
- perl-file-spec
- perl-json
- perl-lwp-simple
- perl-findbin
- blast >=2.6
run:
- libgcc # [linux]
- perl
- perl-bioperl >=1.6.924
- perl-file-slurp
- perl-text-csv
- perl-list-moreutils
- perl-file-spec
- perl-json
- perl-lwp-simple
- perl-findbin
- blast >=2.6
- zlib
- unzip
- emboss
- entrez-direct
- libgcc # [linux]
- perl
- perl-bioperl >=1.6.924
- perl-file-slurp
- perl-text-csv
- perl-list-moreutils
- perl-file-spec
- perl-json
- perl-lwp-simple
- perl-findbin
- blast >=2.6
- zlib {{CONDA_ZLIB}}*
- unzip
- emboss
- entrez-direct

test:
commands:
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2 changes: 1 addition & 1 deletion recipes/addrg/meta.yaml
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Expand Up @@ -5,7 +5,7 @@ package:
version: {{ version }}

build:
number: 0
number: 1
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htslib is not pinned

skip: False

source:
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10 changes: 5 additions & 5 deletions recipes/agg/meta.yaml
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Expand Up @@ -6,7 +6,7 @@ package:
version: {{ version }}

build:
number: 0
number: 1

source:
fn: {{ name|lower }}_{{ version }}.tar.gz
Expand All @@ -15,12 +15,12 @@ source:

requirements:
build:
- gcc
- zlib
- gcc
- zlib {{CONDA_ZLIB}}*

run:
- libgcc
- zlib
- libgcc
- zlib {{CONDA_ZLIB}}*

test:
commands:
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2 changes: 1 addition & 1 deletion recipes/alfred/0.1.2/meta.yaml
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Expand Up @@ -11,7 +11,7 @@ source:
- Makefile.patch

build:
number: 1
number: 3
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2

string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}}
skip: True # [osx]

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2 changes: 1 addition & 1 deletion recipes/alfred/0.1.3/meta.yaml
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Expand Up @@ -11,7 +11,7 @@ source:
- Makefile.patch

build:
number: 1
number: 2
string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}}
skip: True # [osx]

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2 changes: 1 addition & 1 deletion recipes/alfred/meta.yaml
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Expand Up @@ -11,7 +11,7 @@ source:
- Makefile.patch

build:
number: 1
number: 3
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2

string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}}
skip: True # [osx]

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6 changes: 3 additions & 3 deletions recipes/align-it/1.0.3/meta.yaml
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Expand Up @@ -4,7 +4,7 @@ about:
summary: "Align-it is a tool to align molecules according to their pharmacophores. A pharmacophore is an abstract concept based on the specific interactions observed in drug-receptor interactions: hydrogen bonding, charge transfer, electrostatic and hydrophobic interactions."

build:
number: 3
number: 4
skip: True # [osx]

package:
Expand All @@ -16,12 +16,12 @@ requirements:
- gcc # [linux]
- llvm # [osx]
- openbabel ==2.4.1
- zlib
- zlib {{CONDA_ZLIB}}*
- cmake
run:
- openbabel ==2.4.1
- libgcc # [linux]
- zlib
- zlib {{CONDA_ZLIB}}*

source:
fn: align-it-1.0.3.tar.gz
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5 changes: 2 additions & 3 deletions recipes/allegro/meta.yaml
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@@ -1,6 +1,6 @@
package:
name: allegro
version: 2
version: 3

source:
fn: allegro2-2017-10-11.tar.gz
Expand All @@ -17,8 +17,7 @@ source:


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

requirements:
build:
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6 changes: 3 additions & 3 deletions recipes/angsd/meta.yaml
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@@ -1,7 +1,7 @@
{% set version = "0.910" %}

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

about:
Expand All @@ -15,12 +15,12 @@ package:

requirements:
build:
- htslib
- htslib {{ CONDA_HTSLIB }}*
- gcc # [not osx]
- llvm # [osx]
run:
- libgcc # [not osx]
- htslib
- htslib {{ CONDA_HTSLIB }}*

test:
commands:
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6 changes: 3 additions & 3 deletions recipes/aria2/meta.yaml
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Expand Up @@ -8,14 +8,14 @@ source:
md5: 0a28844c8db660d6a20d8a34ae4b0f37

build:
number: 0
number: 1

requirements:
build:
- gcc # [linux]
- llvm # [osx]
- pkg-config # [osx]
- zlib
- zlib {{CONDA_ZLIB}}*
- openssl # [linux]
- sqlite
- libssh2
Expand All @@ -24,7 +24,7 @@ requirements:

run:
- libgcc # [linux]
- zlib
- zlib {{CONDA_ZLIB}}*
- openssl # [linux]
- sqlite
- libssh2
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6 changes: 3 additions & 3 deletions recipes/ariba/meta.yaml
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Expand Up @@ -11,7 +11,7 @@ source:

build:
skip: True # [py27]
number: 0
number: 1

requirements:
build:
Expand All @@ -24,7 +24,7 @@ requirements:
- pysam >=0.9.1
- pymummer >=0.10.2
- gcc
- zlib
- zlib {{CONDA_ZLIB}}*

run:
- python
Expand All @@ -41,7 +41,7 @@ requirements:
- mummer >=3.23
- spades >=3.5.0
- libgcc
- zlib
- zlib {{CONDA_ZLIB}}*

test:
imports:
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2 changes: 1 addition & 1 deletion recipes/asn2gb/meta.yaml
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Expand Up @@ -16,7 +16,7 @@ source:
sha256: 4b6ac3831061bc8f8c8adb011fe58c8741402a9c21c95af395aa98154c9ab775 # [linux]

build:
number: 0
number: 1
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pinning on run-only dep can be removed (needs bioconda/bioconda-utils#264 to make linter happy)


requirements:
run:
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6 changes: 3 additions & 3 deletions recipes/assemblyutility/meta.yaml
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Expand Up @@ -6,7 +6,7 @@ package:
version: {{ version }}

build:
number: 0
number: 1

source:
fn: {{ name|lower }}_{{ version }}.tar.gz
Expand All @@ -17,11 +17,11 @@ requirements:
build:
- gcc # [not osx]
- llvm # [osx]
- zlib
- zlib {{CONDA_ZLIB}}*

run:
- libgcc # [not osx]
- zlib
- zlib {{CONDA_ZLIB}}*

test:
commands:
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2 changes: 1 addition & 1 deletion recipes/augustus/meta.yaml
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Expand Up @@ -17,7 +17,7 @@ source:
- patches/compileSpliceCands.Makefile.patch

build:
number: 2
number: 3
string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}}
skip: True # [osx]

Expand Down
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