CVS commit: pkgsrc/biology/microsynteny-tools

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sun Nov  5 17:59:23 UTC 2023

Added Files:
        pkgsrc/biology/microsynteny-tools: DESCR Makefile PLIST distinfo

Log Message:
biology/microsynteny-tools: Exploring microsyntenic differences

Microsynteny tools is a suite of fast, memory-efficient programs for
exploring microsyntenic relationships between genes.
The tools are designed to allow real-time exploration of gene
landscapes across species via the command line and shell scripts.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/microsynteny-tools/DESCR \
    pkgsrc/biology/microsynteny-tools/Makefile \
    pkgsrc/biology/microsynteny-tools/PLIST \
    pkgsrc/biology/microsynteny-tools/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/microsynteny-tools/DESCR
diff -u /dev/null pkgsrc/biology/microsynteny-tools/DESCR:1.1
--- /dev/null   Sun Nov  5 17:59:23 2023
+++ pkgsrc/biology/microsynteny-tools/DESCR     Sun Nov  5 17:59:23 2023
@@ -0,0 +1,4 @@
+Microsynteny tools is a suite of fast, memory-efficient programs for
+exploring microsyntenic relationships between genes.
+The tools are designed to allow real-time exploration of gene
+landscapes via the command line and shell scripts.
Index: pkgsrc/biology/microsynteny-tools/Makefile
diff -u /dev/null pkgsrc/biology/microsynteny-tools/Makefile:1.1
--- /dev/null   Sun Nov  5 17:59:23 2023
+++ pkgsrc/biology/microsynteny-tools/Makefile  Sun Nov  5 17:59:23 2023
@@ -0,0 +1,23 @@
+# $NetBSD: Makefile,v 1.1 2023/11/05 17:59:23 bacon Exp $
+
+DISTNAME=      microsynteny-tools-0.1.0.175
+CATEGORIES=    biology
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=auerlab/}
+GITHUB_TAG=    c471264f8df1fd73621973737d74f4f48e8eb9d1
+
+OWNER=         bacon%NetBSD.org@localhost
+HOMEPAGE=      https://github.com/auerlab/microsynteny-tools
+COMMENT=       Tools for exploring microsyntenic differences among species
+LICENSE=       2-clause-bsd
+
+DEPENDS+=      curl>0:../../www/curl
+DEPENDS+=      ncbi-blast+>0:../../biology/ncbi-blast+
+DEPENDS+=      ${PYPKGPREFIX}-dna-features-viewer>0:../../biology/py-dna-features-viewer
+DEPENDS+=      auto-admin>0:../../sysutils/auto-admin
+DEPENDS+=      biolibc-tools>0:../../biology/biolibc-tools
+
+REPLACE_PYTHON=        Scripts/*.py
+
+.include "../../biology/biolibc/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/microsynteny-tools/PLIST
diff -u /dev/null pkgsrc/biology/microsynteny-tools/PLIST:1.1
--- /dev/null   Sun Nov  5 17:59:23 2023
+++ pkgsrc/biology/microsynteny-tools/PLIST     Sun Nov  5 17:59:23 2023
@@ -0,0 +1,31 @@
+@comment $NetBSD: PLIST,v 1.1 2023/11/05 17:59:23 bacon Exp $
+bin/ms-add-ortho
+bin/ms-blast
+bin/ms-blast-dbs
+bin/ms-extract
+bin/ms-fetch-cdnas
+bin/ms-fetch-gffs
+bin/ms-fetch-refs
+bin/ms-fish-mammal-intersect
+bin/ms-fish-mammal-percent-changed
+bin/ms-gene-list-extract
+bin/ms-gene-list-fish-mammal-intersect
+bin/ms-gene-list-stack
+bin/ms-intersect
+bin/ms-locate-gene
+bin/ms-menu
+bin/ms-plot
+bin/ms-plot.py
+bin/ms-stack
+bin/ms-stack.py
+libexec/microsynteny-tools/blast-filter.awk
+libexec/microsynteny-tools/conserved-stats.awk
+man/man1/ms-extract.1
+man/man1/ms-intersect.1
+man/man1/ms-plot.1
+man/man1/ms-stack.1
+share/microsynteny-tools/Genes/all-de-ortho.txt
+share/microsynteny-tools/Genes/all-non-de-ortho.txt
+share/microsynteny-tools/Genes/de-tf-ortho.txt
+share/microsynteny-tools/Genes/de-tf-refined-ortho.txt
+share/microsynteny-tools/Genes/non-de-tf-ortho.txt
Index: pkgsrc/biology/microsynteny-tools/distinfo
diff -u /dev/null pkgsrc/biology/microsynteny-tools/distinfo:1.1
--- /dev/null   Sun Nov  5 17:59:23 2023
+++ pkgsrc/biology/microsynteny-tools/distinfo  Sun Nov  5 17:59:23 2023
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1 2023/11/05 17:59:23 bacon Exp $
+
+BLAKE2s (microsynteny-tools-0.1.0.175-c471264f8df1fd73621973737d74f4f48e8eb9d1.tar.gz) = 7d3513a1ba7bb64a35912abee8e152e1d394d4e04b4dca8108c7d82bb37a0a68
+SHA512 (microsynteny-tools-0.1.0.175-c471264f8df1fd73621973737d74f4f48e8eb9d1.tar.gz) = 
19c1bdb1f79392bcf931976cb12aed3bcdbc7d4c3c0ddeaf3ce199f1f827f860c3805457ade1686707ef2e77dd318a1cbd91585351de6a96f46447a95eb6ea18
+Size (microsynteny-tools-0.1.0.175-c471264f8df1fd73621973737d74f4f48e8eb9d1.tar.gz) = 2277767 bytes