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Sat, 21 Sep 2024 03:03:36 GMT (envelope-from git) Date: Sat, 21 Sep 2024 03:03:36 GMT Message-Id: <202409210303.48L33aHE089369@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 89f62deb8a91 - main - biology/fastani: New port: Fast Whole-Genome Similarity (ANI) Estimation List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 89f62deb8a91f3b5b4aebf2d655e70e4ae130680 Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=89f62deb8a91f3b5b4aebf2d655e70e4ae130680 commit 89f62deb8a91f3b5b4aebf2d655e70e4ae130680 Author: Yuri Victorovich AuthorDate: 2024-09-21 00:09:52 +0000 Commit: Yuri Victorovich CommitDate: 2024-09-21 03:03:29 +0000 biology/fastani: New port: Fast Whole-Genome Similarity (ANI) Estimation --- biology/Makefile | 1 + biology/fastani/Makefile | 27 ++++++++++++++++++++++ biology/fastani/distinfo | 5 ++++ biology/fastani/files/patch-CMakeLists.txt | 12 ++++++++++ .../files/patch-src_cgi_core__genome__identity.cpp | 11 +++++++++ biology/fastani/pkg-descr | 4 ++++ 6 files changed, 60 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 0c097ae77b3b..a99bb2d85c12 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -54,6 +54,7 @@ SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack + SUBDIR += fastani SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp diff --git a/biology/fastani/Makefile b/biology/fastani/Makefile new file mode 100644 index 000000000000..5608f01a847f --- /dev/null +++ b/biology/fastani/Makefile @@ -0,0 +1,27 @@ +PORTNAME= fastani +DISTVERSIONPREFIX= v +DISTVERSION= 1.34 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Fast Whole-Genome Similarity (ANI) Estimation +WWW= https://github.com/shenwei356/unikmer/ + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libgsl.so:math/gsl + +USES= cmake:testing + +USE_GITHUB= yes +GH_ACCOUNT= ParBLiSS +GH_PROJECT= FastANI +GH_TUPLE= catchorg:Catch2:359542d:catch/ext/Catch2 + +CMAKE_OFF= BUILD_TESTING +CMAKE_TESTING_ON= BUILD_TESTING # 6 tests fail, see https://github.com/ParBLiSS/FastANI/issues/138 + +PLIST_FILES= bin/fastANI + +.include diff --git a/biology/fastani/distinfo b/biology/fastani/distinfo new file mode 100644 index 000000000000..d53b31741aa9 --- /dev/null +++ b/biology/fastani/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1726871246 +SHA256 (ParBLiSS-FastANI-v1.34_GH0.tar.gz) = dc185cf29b9fa40cdcc2c83bb48150db46835e49b9b64a3dbff8bc4d0f631cb1 +SIZE (ParBLiSS-FastANI-v1.34_GH0.tar.gz) = 3899028 +SHA256 (catchorg-Catch2-359542d_GH0.tar.gz) = 607bf5322291859a136b2580151f41897335e91c51fe0c4dd3950093ff96244b +SIZE (catchorg-Catch2-359542d_GH0.tar.gz) = 1031988 diff --git a/biology/fastani/files/patch-CMakeLists.txt b/biology/fastani/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..037ee9938029 --- /dev/null +++ b/biology/fastani/files/patch-CMakeLists.txt @@ -0,0 +1,12 @@ +--- CMakeLists.txt.orig 2023-07-28 20:41:45 UTC ++++ CMakeLists.txt +@@ -68,7 +68,8 @@ if(${BUILD_TESTING}) + Catch2::Catch2 Catch2::Catch2WithMain + ZLIB::ZLIB GSL::gsl GSL::gslcblas + ${OpenMP_CXX_LIBRARIES} +- gcov) ++ --coverage -g -O0 -fprofile-arcs -ftest-coverage ++ ) + catch_discover_tests(fastANITest) + file(COPY tests/data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) + add_custom_target(lcov lcov -c -d .. -o fastANITest.out diff --git a/biology/fastani/files/patch-src_cgi_core__genome__identity.cpp b/biology/fastani/files/patch-src_cgi_core__genome__identity.cpp new file mode 100644 index 000000000000..050a0942eb2d --- /dev/null +++ b/biology/fastani/files/patch-src_cgi_core__genome__identity.cpp @@ -0,0 +1,11 @@ +--- src/cgi/core_genome_identity.cpp.orig 2024-09-20 22:30:43 UTC ++++ src/cgi/core_genome_identity.cpp +@@ -10,6 +10,8 @@ + #include + #include + ++#include ++ + //Own includes + #include "map/include/map_parameters.hpp" + #include "map/include/base_types.hpp" diff --git a/biology/fastani/pkg-descr b/biology/fastani/pkg-descr new file mode 100644 index 000000000000..78c6e5dbbf54 --- /dev/null +++ b/biology/fastani/pkg-descr @@ -0,0 +1,4 @@ +FastANI is developed for fast alignment-free computation of whole-genome Average +Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of +orthologous gene pairs shared between two microbial genomes. FastANI supports +pairwise comparison of both complete and draft genome assemblies.