Merge branch 'master' into add_tttrlib

bioconda · Nov 12, 2024 · 5441df0 · 5441df0
2 parents c239340 + d29672a
commit 5441df0
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diff --git a/recipes/argo/meta.yaml b/recipes/argo/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "argo" %}
-{% set version = "0.1.1" %}
+{% set version = "0.1.2" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://github.com/xinehc/argo/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 9ddc3bea602e3bdcd3518bb3ecd7795b680addaa513eff0fff83e1010ba4e253
+  sha256: 71f9b113efc07df0101887c1c7450ca12f77b120fd9ebd841ddfdba1b7ff2fe0
 
 build:
   noarch: python
@@ -19,6 +19,7 @@ build:
 requirements:
   host:
     - pip
+    - setuptools
     - python >=3.7
   run:
     - python >=3.7
@@ -36,7 +37,7 @@ about:
   home: https://github.com/xinehc/argo
   license: MIT
   license_family: MIT
-  summary: 'Argo: species-resolved profiling of antibiotic resistant genes with long-read metagenomics'
+  summary: 'Argo: species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping'
 
 extra:
   recipe-maintainers:

diff --git a/recipes/aspera-cli/build.sh b/recipes/aspera-cli/build.sh
@@ -7,7 +7,7 @@ mkdir -p $GEM_HOME
 gem build aspera-cli.gemspec
 gem install --install-dir $GEM_HOME --bindir $GEM_HOME/bin ${PKG_NAME}-${PKG_VERSION}.gem
 gem_path=$GEM_HOME/gems/${PKG_NAME}-${PKG_VERSION}
-cp -r $SRC_DIR/* $gem_path
+cp -rf $SRC_DIR/* $gem_path
 rm $gem_path/{conda_build,build_env_setup}.sh
 tail -n+3 bin/ascli > $gem_path/bin/ascli
 tail -n+3 bin/asession > $gem_path/bin/asession
@@ -25,9 +25,6 @@ EOF
 echo "$(cat header.txt $gem_path/bin/ascli)" > $gem_path/bin/ascli
 echo "$(cat header.txt $gem_path/bin/asession)" > $gem_path/bin/asession
 
-ln -s $gem_path/bin/* $PREFIX/bin
+ln -sf $gem_path/bin/* $PREFIX/bin
 
-export ASCLI_HOME="$PREFIX/etc/aspera"
-ascli conf ascp install && ascli config ascp info 
-cp $ASCLI_HOME/aspera-license .
-ln -s $ASCLI_HOME/{ascp,aspera-license} $PREFIX/bin
+ascli conf ascp install && ascli config ascp info
diff --git a/recipes/aspera-cli/meta.yaml b/recipes/aspera-cli/meta.yaml
@@ -1,23 +1,21 @@
 {% set name = "aspera-cli" %}
-{% set version = "4.14.0" %}
+{% set version = "4.19.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   - url: https://github.com/IBM/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-    sha256: b46df368df71ad926605e85ea4b61b9e48335cce8be31ac04d97ee6f71109f03
+    sha256: e4f9eb47510094132ff02960764254dfc322f1a16c9ad2b8abc60a54e5e21da1
 
 build:
   noarch: generic
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('aspera-cli', max_pin="x") }}
 
 requirements:
-  build:
-    - ruby >=3
   host:
     - ruby >=3
   run:
@@ -26,16 +24,15 @@ requirements:
 test:
   commands:
     - ascli -h
-    - ascp -h
 
 about:
-  home: https://github.com/IBM/aspera-cli
-  license: Apache-2.0
-  license_file: 
-    - LICENSE
-    - aspera-license
-  summary: "Command Line Interface for IBM Aspera products"
-  dev_url: https://github.com/IBM/aspera-cli
+  home: "https://github.com/IBM/aspera-cli"
+  license: "Apache-2.0"
+  license_file: LICENSE
+  license_family: APACHE
+  summary: "Command Line Interface for IBM Aspera products."
+  dev_url: "https://github.com/IBM/aspera-cli"
+  doc_url: "https://www.rubydoc.info/gems/aspera-cli"
 
 extra:
   recipe-maintainers:

diff --git a/recipes/cd-hit/build.sh b/recipes/cd-hit/build.sh
@@ -1,26 +1,28 @@
-#!/bin/sh
+#!/bin/bash
 
-export CFLAGS="-I$PREFIX/include"
-export CPPFLAGS="-I$PREFIX/include"
-export CXXFLAGS="-I$PREFIX/include"
-export LDFLAGS="-L$PREFIX/lib"
+mkdir -p $PREFIX/bin
+
+export CFLAGS="${CFLAGS} -O3"
+export CPPFLAGS="${CPPFLAGS} -I$PREFIX/include"
+export CXXFLAGS="${CXXFLAGS} -O3 -I$PREFIX/include"
+export LDFLAGS="${LDFLAGS} -L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
 sed -i.bak 's/^CC =$//g' Makefile
 sed -i.bak 's/^#LDFLAGS.*//g' Makefile
-
+rm -rf *.bak
 
 if [[ "$OSTYPE" == "darwin"* ]]; then
   #Lines below is commented out until fix provided for OPENMP support on OS X for this program
 
   CCFLAGS="$CCFLAGS -Wl,-rpath ${PREFIX}/lib -L${PREFIX}/lib -I${PREFIX}/include -fopenmp"
   sed -i.bak 's/CCFLAGS = -fopenmp/CCFLAGS += -fopenmp/g' Makefile
+  rm -rf *.bak
   LDFLAGS="$LDFLAGS -stdlib=libc++"
 
   make CC=$CXX openmp=no MAX_SEQ=1000000
 else
   make CC=$GXX MAX_SEQ=1000000
 fi
-
-mkdir -p $PREFIX/bin 
-make install PREFIX=$PREFIX/bin 
+
+make install PREFIX="$PREFIX/bin"