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update spades to 3.13.0 #12408

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Nov 30, 2018
Merged

update spades to 3.13.0 #12408

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ecaa820
update spades to 3.13.0
notestaff Nov 28, 2018
8823b93
spades: removed dipspades; added 3.12.0 recipe in subdir
notestaff Nov 29, 2018
a522218
bumped build number for 3.11.1 due to CI failure
notestaff Nov 29, 2018
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2 changes: 1 addition & 1 deletion recipes/spades/3.11.1/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ source:
sha256: 3ab85d86bf7d595bd8adf11c971f5d258bbbd2574b7c1703b16d6639a725b474 # [linux]

build:
number: 2
number: 3
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requirements:
build:
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12 changes: 12 additions & 0 deletions recipes/spades/3.12.0/build.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
#!/bin/bash

set -e -o pipefail

outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
mkdir -p $outdir
mkdir -p $PREFIX/bin

cp -r bin $outdir
cp -r share $outdir

ln -s $outdir/bin/* $PREFIX/bin
49 changes: 49 additions & 0 deletions recipes/spades/3.12.0/meta.yaml
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@@ -0,0 +1,49 @@
{% set version = "3.12.0" %}
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package:
name: spades
version: {{ version }}

source:
# We currently cannot build SPAdes from source, because it requires g++ 5.3.1 or later,
# which bioconda does not yet support. Therefore, we fetch the statically compiled binaries.
url: https://github.com/ablab/spades/releases/download/v{{ version }}/SPAdes-{{ version }}-Darwin.tar.gz # [osx]
sha256: e2a4f589c190767310545300386c7e2841ebdfe3775850cd52879ef01d376575 # [osx]
url: https://github.com/ablab/spades/releases/download/v{{ version }}/SPAdes-{{ version }}-Linux.tar.gz # [linux]
sha256: 5e8988b0cfd8b5a84b718e1e5af21524c7b1369bcba337dfebeed9c22a4f7141 # [linux]

build:
number: 1

requirements:
run:
- python

test:
commands:
- spades.py --version
- rnaspades.py --version
- truspades.py --version
- dipspades.py --version
- metaspades.py --version
- plasmidspades.py --version
- spades.py --test && rm -rf spades_test
- spades-kmercount -h

about:
home: http://cab.spbu.ru/software/spades/
license: GPLv2
license_family: GPL
license_file: share/spades/LICENSE
summary: |
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
dev_url: https://github.com/ablab/spades
doc_url: http://cab.spbu.ru/files/release{{version}}/manual.html
extra:
recipe-maintainers:
- druvus
- notestaff
identifiers:
- biotools:Spades
- doi:10.1089/cmb.2012.0021
- doi:10.1101/gr.213959.116
9 changes: 4 additions & 5 deletions recipes/spades/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
{% set version = "3.12.0" %}
{% set version = "3.13.0" %}

package:
name: spades
Expand All @@ -8,12 +8,12 @@ source:
# We currently cannot build SPAdes from source, because it requires g++ 5.3.1 or later,
# which bioconda does not yet support. Therefore, we fetch the statically compiled binaries.
url: https://github.com/ablab/spades/releases/download/v{{ version }}/SPAdes-{{ version }}-Darwin.tar.gz # [osx]
sha256: e2a4f589c190767310545300386c7e2841ebdfe3775850cd52879ef01d376575 # [osx]
sha256: 86dac86962b6d26891eb9b1d173d8dd5ce957482013880f6d75b751b7bb274a0 # [osx]
url: https://github.com/ablab/spades/releases/download/v{{ version }}/SPAdes-{{ version }}-Linux.tar.gz # [linux]
sha256: 5e8988b0cfd8b5a84b718e1e5af21524c7b1369bcba337dfebeed9c22a4f7141 # [linux]
sha256: 3666b256e2239adbdf9d8b3e3e6a60b2d8d51878b892ea6a821b033a5ef0d03b # [linux]

build:
number: 1
number: 0

requirements:
run:
Expand All @@ -24,7 +24,6 @@ test:
- spades.py --version
- rnaspades.py --version
- truspades.py --version
- dipspades.py --version
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- metaspades.py --version
- plasmidspades.py --version
- spades.py --test && rm -rf spades_test
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