Merge branch 'master' into update_my_recipe2

bioconda · Nov 18, 2024 · f183729 · f183729
2 parents 4a1412a + 5c6d47a
commit f183729
Show file tree

Hide file tree

Showing 12 changed files with 196 additions and 102 deletions.
diff --git a/recipes/biobambam/build.sh b/recipes/biobambam/build.sh
@@ -1,4 +1,9 @@
 #!/bin/bash
 set -eu
-./configure --prefix=${PREFIX}
+
+autoreconf -if
+./configure --prefix="${PREFIX}" CXX="${CXX}" \
+	--with-libmaus2 --with-xerces-c --with-gmp \
+	CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
+	LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 make install
diff --git a/recipes/biobambam/meta.yaml b/recipes/biobambam/meta.yaml
@@ -1,18 +1,18 @@
 {% set name = "biobambam" %}
-{% set version = "2.0.183" %}
-{% set datestamp = "20210802180148" %}
-{% set sha256hash = "8712ceac509c389111b01dc3429f673dc0f8b77cb2bc48a1ebcf17f6888b2945" %}
+{% set version = "2.0.185" %}
+{% set datestamp = "20221211202123" %}
+{% set sha256 = "e405421e869ac7220c3a7e5da0d24a3c7b4c7b1807e044a439fe68efc88a1f2a" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://gitlab.com/german.tischler/biobambam2/-/archive/{{ version }}-release-{{ datestamp }}/biobambam2-{{ version }}-release-{{ datestamp }}.tar.gz
-  sha256: {{ sha256hash }}
+  sha256: {{ sha256 }}
 
 build:
-  number: 4
+  number: 0
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
@@ -21,19 +21,33 @@ requirements:
   build:
     - make
     - {{ compiler('cxx') }}
+    - autoconf
+    - automake
+    - libtool
+    - pkg-config
   host:
-    - libmaus2 >=2.0.810
+    - libmaus2 >=2.0.813
+    - gmp
+    - xerces-c
+    - zlib
+  run:
+    - libmaus2 >=2.0.813
 
 test:
   commands:
     - bamsormadup --help
     - bamtofastq --help
+
 about:
   home: https://gitlab.com/german.tischler/biobambam2
-  license: GPLv3
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: GPLv3
-  summary: Tools for early stage alignment file processing
+  summary: "Tools for early stage alignment file processing."
+  dev_url: https://gitlab.com/german.tischler/biobambam2
 
 extra:
   additional-platforms:
-    - linux-aarch64
+    - linux-aarch64
+  identifiers:
+    - biotools:biobambam
diff --git a/recipes/cnvkit/meta.yaml b/recipes/cnvkit/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "cnvkit" %}
-{% set version = "0.9.11" %}
+{% set version = "0.9.12" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/etal/cnvkit/archive/v{{ version }}.tar.gz
-  sha256: 1763936427184270108fd51219ebc82f542e28339bdec587579b8745f61179a8
+  sha256: 39d65ba3d9c541dfd80986ace298b2d521067d1b81edef7169196b8dcc5d63d5
 
 build:
   noarch: python
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - bioconductor-dnacopy
@@ -49,13 +50,13 @@ test:
     - cnvkit.py -h
 
 about:
-  home: https://github.com/etal/cnvkit
-  license: Apache-2.0
+  home: "https://github.com/etal/cnvkit"
+  license: "Apache-2.0"
   license_family: APACHE
   license_file: LICENSE
-  summary: Copy number variant detection from high-throughput sequencing
-  dev_url: https://github.com/etal/cnvkit
-  doc_url: https://cnvkit.readthedocs.io/en/stable/
+  summary: "Copy number variant detection from high-throughput sequencing."
+  dev_url: "https://github.com/etal/cnvkit"
+  doc_url: "https://cnvkit.readthedocs.io/en/stable"
 
 extra:
   identifiers:

diff --git a/recipes/isoquant/meta.yaml b/recipes/isoquant/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "IsoQuant" %}
-{% set version = "3.6.1" %}
-{% set sha256 = "6d16e47e9ca45f9a0d029940d5b84e03038d9ba3d640945e3a5087acfd7ed56d" %}
+{% set version = "3.6.2" %}
+{% set sha256 = "b742fe460b44d0d9feb967938176e707cfe4f281c53bf4fe04af2440c31e7862" %}
 
 package:
   name: {{ name | lower }}

diff --git a/recipes/libmaus2/build.sh b/recipes/libmaus2/build.sh
@@ -1,10 +1,14 @@
 #!/bin/bash
 set -eu
-export LIBS="-lstdc++fs -lcurl"
+export LIBS="-lstdc++fs -lcurl -lz -ldeflate"
 
-./configure --prefix $PREFIX --with-snappy --with-io_lib
+autoreconf -if
+./configure --prefix="${PREFIX}" CXX="${CXX}" CC="${CC}" \
+	LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \
+	CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
+	--with-snappy --with-io_lib --with-libdeflate \
+	--with-libsecrecy --with-nettle \
+	--with-lzma --with-gmp
 
-cat config.log
-
-make -j${CPU_COUNT}
+make -j"${CPU_COUNT}"
 make install
diff --git a/recipes/libmaus2/meta.yaml b/recipes/libmaus2/meta.yaml
@@ -1,7 +1,7 @@
 {% set name = "libmaus2" %}
-{% set version = "2.0.810" %}
-{% set datestamp = "20220216151520" %}
-{% set sha256hash = "6639289aba6bbece3057ab7d1782a1b94b80a9ae22fc3d136a78ba8f7b9edaee" %}
+{% set version = "2.0.813" %}
+{% set datestamp = "20221210220409" %}
+{% set sha256 = "4125f8daefd6900185675026498369457088e25e81029597659249be49cd5261" %}
 
 package:
   name: {{ name }}
@@ -10,47 +10,61 @@ package:
 build:
   # There's some issue with clang
   skip: True  # [osx]
-  number: 6
+  number: 0
   run_exports:
-    - {{ pin_subpackage('libmaus2', max_pin='x.x') }}
+    - {{ pin_subpackage('libmaus2', max_pin='x') }}
 
 source:
   url: https://gitlab.com/german.tischler/libmaus2/-/archive/{{ version }}-release-{{ datestamp }}/libmaus2-{{ version }}-release-{{ datestamp }}.tar.gz
-  sha256: {{ sha256hash }}
-  patches:
+  sha256: {{ sha256 }}
+  #patches:
     # Until gcc >=8 is being used
-    - patch
+    #- patch
 
 requirements:
   build:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
+    - autoconf
+    - automake
+    - libtool
+    - pkg-config
   host:
     - boost-cpp
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
     - libcurl
     # snappy 1.1.9 introduced a binary incompatible build change (https://github.com/mhx/dwarfs/issues/56#issuecomment-896857211)
     # enabling -fno-rtti. libmaus needs typeid, which is only available with activated rtti.
     # Hence, we stick with snappy 1.1.8
-    - snappy =1.1.8 
+    - snappy =1.1.8
     - staden_io_lib >=1.14.14
+    - libdeflate
+    - gmp
+    - nettle
+    - zlib
   run:
     - boost-cpp
-    - libcurl
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
     - snappy =1.1.8
     - staden_io_lib >=1.14.14
-  ignore_run_exports:
-    - snappy
-
-about:
-  home: https://gitlab.com/german.tischler/libmaus2
-  license: GPL3
-  summary: collection of data structures and algorithms for NGS data
 
 test:
   commands:
     - echo
 
+about:
+  home: https://gitlab.com/german.tischler/libmaus2
+  license: GPL-3.0-or-later
+  license_family: GPL3
+  license_file: GPLv3
+  summary: "Collection of data structures and algorithms for NGS data."
+  dev_url: https://gitlab.com/german.tischler/libmaus2
+
 extra:
   additional-platforms:
     - linux-aarch64
+  identifiers:
+    - biotools:libmaus
diff --git a/recipes/libmaus2/patch b/recipes/libmaus2/patch
@@ -127,36 +127,6 @@ index 134ff0f4..b8fcfe88 100644
 
  				setHWTReq  (p_hwt_req.string());
  				setHWT     (p_hwt.string());
-diff --git a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-index 1e8e53b9..a91d1916 100644
---- a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-+++ b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-@@ -111,11 +111,11 @@ namespace libmaus2
- 				// base tmp directory name
- 				std::string tmpdirname;
- 				// tmpdirname as path object
--				std::filesystem::path tmppath;
--				std::filesystem::path base_tmp_path;
--				std::filesystem::path ds_tmp_path_base_ds_tmp;
--				std::filesystem::path merge_tmp_path;
--				std::filesystem::path ds_tmp_path_merge_ds_tmp;
-+				std::experimental::filesystem::path tmppath;
-+				std::experimental::filesystem::path base_tmp_path;
-+				std::experimental::filesystem::path ds_tmp_path_base_ds_tmp;
-+				std::experimental::filesystem::path merge_tmp_path;
-+				std::experimental::filesystem::path ds_tmp_path_merge_ds_tmp;
-
- 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSbase;
- 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSmerge;
-@@ -333,7 +333,7 @@ namespace libmaus2
- 					return C;
- 				}
-
--				static std::filesystem::path ensureDirectory(std::filesystem::path path)
-+				static std::experimental::filesystem::path ensureDirectory(std::experimental::filesystem::path path)
- 				{
- 					libmaus2::aio::OutputStreamFactoryContainer::mkdirp(path.string(),0700);
- 					return path;
 diff --git a/src/libmaus2/util/ArgInfo.cpp b/src/libmaus2/util/ArgInfo.cpp
 index 3802cbb7..8ecd441c 100644
 --- a/src/libmaus2/util/ArgInfo.cpp
@@ -267,6 +237,42 @@ index 2ff71e4a..0714e612 100644
  				dictpath /= digest;
 
  				std::cerr << "[V] writing " << dictpath << " for " << pat.sid << " in " << ref << std::endl;
--- 
-2.33.0
-
+diff --git a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
+index 180f466..0b69f74 100644
+--- a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
++++ b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
+@@ -111,11 +111,11 @@ namespace libmaus2
+ 				// base tmp directory name
+ 				std::string tmpdirname;
+ 				// tmpdirname as path object
+-				std::filesystem::path tmppath;
+-				std::filesystem::path base_tmp_path;
+-				std::filesystem::path ds_tmp_path_base_ds_tmp;
+-				std::filesystem::path merge_tmp_path;
+-				std::filesystem::path ds_tmp_path_merge_ds_tmp;
++				std::experimental::filesystem::path tmppath;
++				std::experimental::filesystem::path base_tmp_path;
++				std::experimental::filesystem::path ds_tmp_path_base_ds_tmp;
++				std::experimental::filesystem::path merge_tmp_path;
++				std::experimental::filesystem::path ds_tmp_path_merge_ds_tmp;
+
+ 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSbase;
+ 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSmerge;
+@@ -333,7 +333,7 @@ namespace libmaus2
+ 					return C;
+ 				}
+
+-				static std::filesystem::path ensureDirectory(std::filesystem::path path)
++				static std::experimental::filesystem::path ensureDirectory(std::experimental::filesystem::path path)
+ 				{
+ 					libmaus2::aio::OutputStreamFactoryContainer::mkdirp(path.string(),0700);
+ 					return path;
+@@ -358,7 +358,7 @@ namespace libmaus2
+ 					preisasamplingrate(std::min(options.maxpreisasamplingrate,blocksizeprevtwo)),
+ 					V_boundedlcpblockvalues(new libmaus2::util::AtomicArray<uint64_t>(numblocks,0)),
+ 					// tmp directory name
+-					tmpdirname(ensureDirectory(std::filesystem::path(options.tmpfilenamebase + "_tmpdir")).string()),
++					tmpdirname(ensureDirectory(std::experimental::filesystem::path(options.tmpfilenamebase + "_tmpdir")).string()),
+ 					// path object for tmp directory name
+ 					tmppath(tmpdirname),
+ 					base_tmp_path(ensureDirectory(tmppath / "base_tmp")),