CVS commit: pkgsrc/biology/fasda

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Aug 12 15:02:00 UTC 2023

Modified Files:
        pkgsrc/biology/fasda: Makefile PLIST distinfo

Log Message:
biology/fasda: Update to 0.1.4

Add --debug
Replace --map-gene with --feature-type for more flexibility
Use extended REs for gff3 feature selection
(default = RNA$|transcript$|gene_segment$, same as transcript in GTF)
Add --output-dir
Support |-separated ID aliases (report last alias)
Support outsourcing abundance calculation (default = stringtie)
Several bug fixes and minor enhancements

Changes: https://github.com/auerlab/fasda/releases


To generate a diff of this commit:
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/fasda/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/fasda/PLIST \
    pkgsrc/biology/fasda/distinfo

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

Modified files:

Index: pkgsrc/biology/fasda/Makefile
diff -u pkgsrc/biology/fasda/Makefile:1.4 pkgsrc/biology/fasda/Makefile:1.5
--- pkgsrc/biology/fasda/Makefile:1.4   Wed Jun 14 18:45:12 2023
+++ pkgsrc/biology/fasda/Makefile       Sat Aug 12 15:02:00 2023
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.4 2023/06/14 18:45:12 bacon Exp $
+# $NetBSD: Makefile,v 1.5 2023/08/12 15:02:00 bacon Exp $
 
-DISTNAME=      fasda-0.1.3
+DISTNAME=      fasda-0.1.4
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=auerlab/}
 
@@ -9,6 +9,8 @@ HOMEPAGE=       https://github.com/auerlab/fas
 COMMENT=       Fast and simple differential analysis
 LICENSE=       2-clause-bsd
 
+DEPENDS=       stringtie>0:../../biology/stringtie
+
 LDFLAGS.SunOS+=        -lresolv
 
 pre-build:

Index: pkgsrc/biology/fasda/PLIST
diff -u pkgsrc/biology/fasda/PLIST:1.3 pkgsrc/biology/fasda/PLIST:1.4
--- pkgsrc/biology/fasda/PLIST:1.3      Wed Jun 14 18:45:12 2023
+++ pkgsrc/biology/fasda/PLIST  Sat Aug 12 15:02:00 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.3 2023/06/14 18:45:12 bacon Exp $
+@comment $NetBSD: PLIST,v 1.4 2023/08/12 15:02:00 bacon Exp $
 bin/fasda
 libexec/fasda/abundance
 libexec/fasda/fold-change
Index: pkgsrc/biology/fasda/distinfo
diff -u pkgsrc/biology/fasda/distinfo:1.3 pkgsrc/biology/fasda/distinfo:1.4
--- pkgsrc/biology/fasda/distinfo:1.3   Wed Jun 14 18:45:12 2023
+++ pkgsrc/biology/fasda/distinfo       Sat Aug 12 15:02:00 2023
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.3 2023/06/14 18:45:12 bacon Exp $
+$NetBSD: distinfo,v 1.4 2023/08/12 15:02:00 bacon Exp $
 
-BLAKE2s (fasda-0.1.3.tar.gz) = 18a2608788bea222ae0830df8d4a8579dc3082cda6d6b7c6f7a24e68734721fd
-SHA512 (fasda-0.1.3.tar.gz) = 7a14f7ee37f75a37c822db806df5cc994e30514cf18f398e3e6c763981590ba2bcc3451689224345f79ceace99b9a0b6f123c535f976c633e991c86a787b7b1b
-Size (fasda-0.1.3.tar.gz) = 59513 bytes
+BLAKE2s (fasda-0.1.4.tar.gz) = ad32eaef6ed1c5f74812f7af62d5cbb0d665013b1a0221a8bf7236f73a80c0c6
+SHA512 (fasda-0.1.4.tar.gz) = 96837c99035692dc67d23eda814363cd8bdd38bc8924ebec7b63a4b0d30333d77ff822d365ee27c92f598242a73c3ee019948c18eb4a16aee627c2f666a5d467
+Size (fasda-0.1.4.tar.gz) = 65254 bytes