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Fri, 21 Jul 2023 21:39:01 GMT (envelope-from git) Date: Fri, 21 Jul 2023 21:39:01 GMT Message-Id: <202307212139.36LLd1Se007085@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: 04d04b8dafba - main - biology/seqwish: New port: Assembly By Short Sequences: parallel, paired-end sequence assembler List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@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: 04d04b8dafba8cd1a9875fe8f027c1e310d8ed5f Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=04d04b8dafba8cd1a9875fe8f027c1e310d8ed5f commit 04d04b8dafba8cd1a9875fe8f027c1e310d8ed5f Author: Yuri Victorovich AuthorDate: 2023-07-21 21:38:22 +0000 Commit: Yuri Victorovich CommitDate: 2023-07-21 21:38:59 +0000 biology/seqwish: New port: Assembly By Short Sequences: parallel, paired-end sequence assembler --- biology/Makefile | 1 + biology/seqwish/Makefile | 25 ++++++++++++++++++++++ biology/seqwish/distinfo | 3 +++ biology/seqwish/files/patch-CMakeLists.txt | 14 +++++++++++++ biology/seqwish/files/patch-src_main.cpp | 24 +++++++++++++++++++++ biology/seqwish/files/patch-src_tempfile.cpp | 31 ++++++++++++++++++++++++++++ biology/seqwish/pkg-descr | 10 +++++++++ 7 files changed, 108 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index e41e9edcb828..4f426e0a00ca 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -214,6 +214,7 @@ SUBDIR += seqio SUBDIR += seqkit SUBDIR += seqtk + SUBDIR += seqwish SUBDIR += sigviewer SUBDIR += sim4 SUBDIR += slclust diff --git a/biology/seqwish/Makefile b/biology/seqwish/Makefile new file mode 100644 index 000000000000..a34c6f9e1370 --- /dev/null +++ b/biology/seqwish/Makefile @@ -0,0 +1,25 @@ +PORTNAME= seqwish +DISTVERSIONPREFIX= v +DISTVERSION= 0.7.9 +CATEGORIES= biology +MASTER_SITES= https://github.com/ekg/seqwish/releases/download/v${DISTVERSION}/ + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler +WWW= https://www.bcgsc.ca/resources/software/abyss + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= cmake:noninja + +PLIST_FILES= bin/${PORTNAME} + +OPTIONS_DEFINE= OPENMP +OPTIONS_DEFAULT= OPENMP + +OPENMP_CMAKE_BOOL= USE_OPENMP +OPENMP_CXXFLAGS= -fopenmp +OPENMP_BROKEN_OFF= https://github.com/ekg/seqwish/issues/114 + +.include diff --git a/biology/seqwish/distinfo b/biology/seqwish/distinfo new file mode 100644 index 000000000000..5753ca0fb6de --- /dev/null +++ b/biology/seqwish/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1689972439 +SHA256 (seqwish-v0.7.9.tar.gz) = 1ca7ebf02a35ad147c8a2b81f087aaba2deb878fec7acb4deb9f14e932e89d36 +SIZE (seqwish-v0.7.9.tar.gz) = 12116251 diff --git a/biology/seqwish/files/patch-CMakeLists.txt b/biology/seqwish/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..3c6ca1d2757f --- /dev/null +++ b/biology/seqwish/files/patch-CMakeLists.txt @@ -0,0 +1,14 @@ +--- CMakeLists.txt.orig 2023-04-19 15:25:32 UTC ++++ CMakeLists.txt +@@ -256,9 +256,9 @@ target_link_libraries(seqwish + "${sdsl-lite_LIB}/libsdsl.a" + "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" + "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" +- "-latomic" ++ #"-latomic" + Threads::Threads +- jemalloc ++ #jemalloc + z) + if (BUILD_STATIC) + #set(CMAKE_EXE_LINKER_FLAGS "-static") diff --git a/biology/seqwish/files/patch-src_main.cpp b/biology/seqwish/files/patch-src_main.cpp new file mode 100644 index 000000000000..73ff8da2acdb --- /dev/null +++ b/biology/seqwish/files/patch-src_main.cpp @@ -0,0 +1,24 @@ +--- src/main.cpp.orig 2023-07-21 20:57:07 UTC ++++ src/main.cpp +@@ -24,6 +24,8 @@ + #include "version.hpp" + #include "tempfile.hpp" + ++#include ++ + using namespace seqwish; + + int main(int argc, char** argv) { +@@ -116,9 +118,10 @@ int main(int argc, char** argv) { + if (tmp_base) { + temp_file::set_dir(args::get(tmp_base)); + } else { +- char* cwd = get_current_dir_name(); ++ char cwd[MAXPATHLEN]; ++ getwd(cwd); + temp_file::set_dir(std::string(cwd)); +- free(cwd); ++ //free(cwd); + } + + temp_file::set_keep_temp(args::get(keep_temp_files)); diff --git a/biology/seqwish/files/patch-src_tempfile.cpp b/biology/seqwish/files/patch-src_tempfile.cpp new file mode 100644 index 000000000000..7f6c4699400d --- /dev/null +++ b/biology/seqwish/files/patch-src_tempfile.cpp @@ -0,0 +1,31 @@ +--- src/tempfile.cpp.orig 2023-07-21 20:48:46 UTC ++++ src/tempfile.cpp +@@ -3,6 +3,8 @@ + #include + #include "tempfile.hpp" + ++#include ++ + namespace temp_file { + + // We use this to make the API thread-safe +@@ -96,9 +98,10 @@ namespace temp_file { + + // Get the default temp dir from environment variables. + if (temp_dir.empty()) { +- char* cwd = get_current_dir_name(); ++ char cwd[MAXPATHLEN]; ++ getwd(cwd); + temp_dir = std::string(cwd); +- free(cwd); ++ //free(cwd); + /*const char *system_temp_dir = nullptr; + for (const char *var_name : {"TMPDIR", "TMP", "TEMP", "TEMPDIR", "USERPROFILE"}) { + if (system_temp_dir == nullptr) { +@@ -114,4 +117,4 @@ namespace temp_file { + void set_keep_temp(bool setting) { + keep_temp = setting; + } +-} +\ No newline at end of file ++} diff --git a/biology/seqwish/pkg-descr b/biology/seqwish/pkg-descr new file mode 100644 index 000000000000..2267dba52b9f --- /dev/null +++ b/biology/seqwish/pkg-descr @@ -0,0 +1,10 @@ +seqwish implements a lossless conversion from pairwise alignments between +sequences to a variation graph encoding the sequences and their alignments. +As input we typically take all-versus-all alignments, but the exact structure +of the alignment set may be defined in an application specific way. This +algorithm uses a series of disk-backed sorts and passes over the alignment and +sequence inputs to allow the graph to be constructed from very large inputs +that are commonly encountered when working with large numbers of noisy input +sequences. Memory usage during construction and traversal is limited by the use +of sorted disk-backed arrays and succinct rank/select dictionaries to record a +queryable version of the graph.