git: 864d4fdd1804 - main - biology/libgff: GFF/GTF parsing library based on GCLib
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Date: Sun, 05 Dec 2021 20:50:57 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=864d4fdd1804d2d4f46619f781e397b9ccdf1639
commit 864d4fdd1804d2d4f46619f781e397b9ccdf1639
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2021-12-05 20:50:42 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2021-12-05 20:50:42 +0000
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.
---
biology/Makefile | 1 +
biology/libgff/Makefile | 16 ++++++++++++++++
biology/libgff/distinfo | 3 +++
biology/libgff/pkg-descr | 11 +++++++++++
biology/libgff/pkg-plist | 14 ++++++++++++++
5 files changed, 45 insertions(+)
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