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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-12-05 20:50:42 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-12-05 20:50:42 +0000 |
| commit | 864d4fdd1804d2d4f46619f781e397b9ccdf1639 (patch) | |
| tree | b32b902152c04a4fbcf83802a3c18ca863d9ab88 | |
| parent | 316c372c7d133c416ced0bd6b1f21fdd011117eb (diff) | |
| download | ports-864d4fdd1804d2d4f46619f781e397b9ccdf1639.tar.gz ports-864d4fdd1804d2d4f46619f781e397b9ccdf1639.zip | |
biology/libgff: GFF/GTF parsing library based on GCLib
This is an attempt to perform a simple "libraryfication" of the GFF/GTF
parsing code that is used in GFFRead codebase. There are not many
(any?) relatively lightweight GTF/GFF parsers exposing a C++ interface,
and the goal of this library is to provide this functionality without
the necessity of drawing in a heavy-weight dependency like SeqAn. Note:
This library draws directly from the code in GFFRead and GCLib, and
exists primarily to remove functionality (and hence code) that is
unnecessary for our downstream purposes. In the future, it may be
appropriate to just replace this library wholesale with GCLib.
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/libgff/Makefile | 16 | ||||
| -rw-r--r-- | biology/libgff/distinfo | 3 | ||||
| -rw-r--r-- | biology/libgff/pkg-descr | 11 | ||||
| -rw-r--r-- | biology/libgff/pkg-plist | 14 |
5 files changed, 45 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 02ba7b46b286..4e16a737f636 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -78,6 +78,7 @@ SUBDIR += kallisto SUBDIR += lamarc SUBDIR += libbigwig + SUBDIR += libgff SUBDIR += libgtextutils SUBDIR += libneurosim SUBDIR += libnuml diff --git a/biology/libgff/Makefile b/biology/libgff/Makefile new file mode 100644 index 000000000000..6a16d0cd4557 --- /dev/null +++ b/biology/libgff/Makefile @@ -0,0 +1,16 @@ +PORTNAME= libgff +DISTVERSIONPREFIX= v +DISTVERSION= 2.0.0 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= GFF/GTF parsing library based on GCLib + +LICENSE= BSL +LICENSE_FILE= ${WRKSRC}/BoostLicense.txt + +USES= cmake +USE_GITHUB= yes +GH_ACCOUNT= COMBINE-lab + +.include <bsd.port.mk> diff --git a/biology/libgff/distinfo b/biology/libgff/distinfo new file mode 100644 index 000000000000..9bb01692e5c1 --- /dev/null +++ b/biology/libgff/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1631451501 +SHA256 (COMBINE-lab-libgff-v2.0.0_GH0.tar.gz) = 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c +SIZE (COMBINE-lab-libgff-v2.0.0_GH0.tar.gz) = 102152 diff --git a/biology/libgff/pkg-descr b/biology/libgff/pkg-descr new file mode 100644 index 000000000000..762881bedb74 --- /dev/null +++ b/biology/libgff/pkg-descr @@ -0,0 +1,11 @@ +This is an attempt to perform a simple "libraryfication" of the GFF/GTF +parsing code that is used in GFFRead codebase. There are not many +(any?) relatively lightweight GTF/GFF parsers exposing a C++ interface, +and the goal of this library is to provide this functionality without +the necessity of drawing in a heavy-weight dependency like SeqAn. Note: +This library draws directly from the code in GFFRead and GCLib, and +exists primarily to remove functionality (and hence code) that is +unnecessary for our downstream purposes. In the future, it may be +appropriate to just replace this library wholesale with GCLib. + +WWW: https://github.com/COMBINE-lab/libgff diff --git a/biology/libgff/pkg-plist b/biology/libgff/pkg-plist new file mode 100644 index 000000000000..474ea892d185 --- /dev/null +++ b/biology/libgff/pkg-plist @@ -0,0 +1,14 @@ +include/GArgs.h +include/GBase.h +include/GFaSeqGet.h +include/GFastaIndex.h +include/GHash.hh +include/GList.hh +include/GStr.h +include/GVec.hh +include/codons.h +include/gdna.h +include/gff.h +lib/libgff.a +lib/libgff/cmake/libgffConfig.cmake +lib/libgff/cmake/libgffConfigVersion.cmake |