update spades to 3.13.0 (#12408)

* update spades to 3.13.0 * spades: removed dipspades; added 3.12.0 recipe in subdir * bumped build number for 3.11.1 due to CI failure
bioconda · Nov 30, 2018 · 72cb853 · 72cb853
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commit 72cb853
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diff --git a/recipes/spades/3.11.1/meta.yaml b/recipes/spades/3.11.1/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: 3ab85d86bf7d595bd8adf11c971f5d258bbbd2574b7c1703b16d6639a725b474  # [linux]
 
 build:
-  number: 2
+  number: 3
 
 requirements:
   build:

diff --git a/recipes/spades/3.12.0/build.sh b/recipes/spades/3.12.0/build.sh
@@ -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
diff --git a/recipes/spades/3.12.0/meta.yaml b/recipes/spades/3.12.0/meta.yaml
@@ -0,0 +1,49 @@
+{% set version = "3.12.0" %}
+
+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
diff --git a/recipes/spades/meta.yaml b/recipes/spades/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "3.12.0" %}
+{% set version = "3.13.0" %}
 
 package:
   name: spades
@@ -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:
@@ -24,7 +24,6 @@ test:
     - 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