[Gsrc-commit] trunk r10830: update slimsuite to 1.12.0

[Carl Hansen]

------------------------------------------------------------
revno: 10830
revision-id: carlhansen@gnu.org-20241118193320-vk22i36ouu0ak34m
parent: carlhansen@gnu.org-20241118181513-u98g9vxtjh93ql7d
committer: carlhansen@gnu.org
branch nick: trunk
timestamp: Mon 2024-11-18 19:33:20 +0000
message:
  update slimsuite to 1.12.0
modified:
  pkg/bio/slimsuite/Makefile     makefile-20160617195624-kwz1a09vkg4le6fu-184
  pkg/bio/slimsuite/sha256sums   sha256sums-20160617195624-kwz1a09vkg4le6fu-185

=== modified file 'pkg/bio/slimsuite/Makefile'
--- a/pkg/bio/slimsuite/Makefile        2016-06-17 19:57:40 +0000
+++ b/pkg/bio/slimsuite/Makefile        2024-11-18 19:33:20 +0000
@@ -1,6 +1,7 @@
 # Copyright © 2014 Brandon Invergo <brandon@invergo.net>
+# Copyright © 2024 Carl Hansen
 #
-# This file is part of BioSRC.
+# This file is part of BioSRC and GSRC.
 #
 # BioSRC is free software: you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by
@@ -17,67 +18,77 @@
 
 NAME = SLiMSuite
 GARNAME = slimsuite
-GARVERSION = 2014-08-25
-HOME_URL = https://www.southampton.ac.uk/~re1u06/software/packages/slimsuite/
-DESCRIPTION = Programs for the prediction of short linear motifs
+GARVERSION = 1.12.0
+#HOME_URL = https://www.southampton.ac.uk/~re1u06/software/packages/slimsuite/
+HOME_URL = https://slimsuite.blogspot.com
+DESCRIPTION = short linear motif discovery and sequence analysis
 define BLURB
-SLiMSuite contains software for short linear motif analysis.
+SLiMSuite contains software for short linear motif discovery and sequence
+analysis 
 endef
 LICENSE = GPLv2 or later
-CITE = 
+CITE =  Edwards et al. (2020), Methods Mol Biol. 2141:37-72. [PMID: 32696352]
+CITE = Old citation: Edwards RJ & Palopoli N (2015): Methods Mol Biol. 
1268:89-141. [PMID: 25555723]
 
 ######################################################################
+#MASTER_SITES = http://www.southampton.ac.uk/
+#MASTER_SUBDIR = ~re1u06/software/packages/
 
-MASTER_SITES = http://www.southampton.ac.uk/
-MASTER_SUBDIR = ~re1u06/software/packages/
-DISTNAME = $(GARNAME).$(GARVERSION)
-DISTFILES = $(DISTNAME).tar.gz
-WORKSRC = $(WORKDIR)/$(GARNAME)
-INSTALL_SCRIPTS = scripts
+#https://github.com/slimsuite/SLiMSuite/archive/refs/tags/v1.12.0.tar.gz
+MASTER_SITES = https://github.com/
+MASTER_SUBDIR = slimsuite/SLiMSuite/archive/refs/tags/
+#DISTNAME = v$(GARVERSION)
+DISTFILES = v$(GARVERSION).tar.gz
+WORKSRC = $(WORKDIR)/$(NAME)-$(GARVERSION)
 
 BUILDDEPS =
 LIBDEPS =
 
+#INSTALL_SCRIPTS = scripts
 ######################################################################
-
+# now python3ified
+#
+#
+# installation not done yet, ....
+#
 include ../../../gar/gar.mk
 include config.mk
 
-LIBDIR = lib/python2.7/site-packages/seqsuite
-
-pre-install:
-       for f in $(WORKSRC)/extras/*.py $(WORKSRC)/tools/*.py; do \
-               sed -i '1s|#!.*|#!/usr/bin/env python2|' $$f; \
-       done
-       sed -i 's|blastpath=.*|blastpath=$(prefix)/bin|' 
$(WORKSRC)/settings/defaults.ini
-       sed -i 's|clustalw=.*|clustalw=$(prefix)/bin/clustalw|' 
$(WORKSRC)/settings/defaults.ini
-       sed -i 's|iupath=.*|iupath=$(prefix)/bin/iupred|' 
$(WORKSRC)/settings/defaults.ini
-       sed -i 's|pypath=.*|pypath=$(prefix)/$(LIBDIR)/|' 
$(WORKSRC)/settings/defaults.ini
-       sed -i 's|fsa=.*|fsa=$(prefix)/bin/fsa|' 
$(WORKSRC)/settings/defaults.ini
-       sed -i 's|mafft=.*|mafft=$(prefix)/bin/mafft|' 
$(WORKSRC)/settings/defaults.ini
-       sed -i 's|fasttree=.*|fasttree=$(prefix)/bin/FastTree|' 
$(WORKSRC)/settings/defaults.ini
-       sed -i 's|phylip=.*|phylip=$(prefix)/bin/|' 
$(WORKSRC)/settings/defaults.ini
-       sed -i 's|clustalo=.*|clustalo=$(prefix)/bin/clustalo|' 
$(WORKSRC)/settings/defaults.ini
-       sed -i 's|pagan=.*|pagan=$(prefix)/bin/pagan|' 
$(WORKSRC)/settings/defaults.ini
-       $(MAKECOOKIE)
-
-install-scripts:
-       install -d $(packageprefix)/$(LIBDIR)
-       install -d $(packageprefix)/$(LIBDIR)/extras
-       install -d $(packageprefix)/$(LIBDIR)/libraries
-       install -d $(packageprefix)/$(LIBDIR)/settings
-       install -d $(packageprefix)/$(LIBDIR)/tools
-       install -d $(packageprefix)/bin
-       for f in $(WORKSRC)/extras/*; do \
-               install -m755 $$f $(packageprefix)/$(LIBDIR)/extras/`basename 
$$f`; \
-               ln -s $(packagedir)/$(LIBDIR)/extras/`basename $$f` 
$(packageprefix)/bin/`basename $$f .py`; \
-       done
-       for f in $(WORKSRC)/tools/*; do \
-               install -m755 $$f $(packageprefix)/$(LIBDIR)/tools/`basename 
$$f`; \
-               ln -s $(packagedir)/$(LIBDIR)/tools/`basename $$f` 
$(packageprefix)/bin/`basename $$f .py`; \
-       done
-       for f in $(WORKSRC)/libraries/*; do \
-               install -m644 $$f 
$(packageprefix)/$(LIBDIR)/libraries/`basename $$f`; \
-       done
-       install -m644 $(WORKSRC)/settings/defaults.ini 
$(packageprefix)/$(LIBDIR)/settings/defaults.ini
-       $(MAKECOOKIE)
+# LIBDIR = lib/python2.7/site-packages/seqsuite
+# 
+# pre-install:
+#      for f in $(WORKSRC)/extras/*.py $(WORKSRC)/tools/*.py; do \
+#              sed -i '1s|#!.*|#!/usr/bin/env python2|' $$f; \
+#      done
+#      sed -i 's|blastpath=.*|blastpath=$(prefix)/bin|' 
$(WORKSRC)/settings/defaults.ini
+#      sed -i 's|clustalw=.*|clustalw=$(prefix)/bin/clustalw|' 
$(WORKSRC)/settings/defaults.ini
+#      sed -i 's|iupath=.*|iupath=$(prefix)/bin/iupred|' 
$(WORKSRC)/settings/defaults.ini
+#      sed -i 's|pypath=.*|pypath=$(prefix)/$(LIBDIR)/|' 
$(WORKSRC)/settings/defaults.ini
+#      sed -i 's|fsa=.*|fsa=$(prefix)/bin/fsa|' 
$(WORKSRC)/settings/defaults.ini
+#      sed -i 's|mafft=.*|mafft=$(prefix)/bin/mafft|' 
$(WORKSRC)/settings/defaults.ini
+#      sed -i 's|fasttree=.*|fasttree=$(prefix)/bin/FastTree|' 
$(WORKSRC)/settings/defaults.ini
+#      sed -i 's|phylip=.*|phylip=$(prefix)/bin/|' 
$(WORKSRC)/settings/defaults.ini
+#      sed -i 's|clustalo=.*|clustalo=$(prefix)/bin/clustalo|' 
$(WORKSRC)/settings/defaults.ini
+#      sed -i 's|pagan=.*|pagan=$(prefix)/bin/pagan|' 
$(WORKSRC)/settings/defaults.ini
+#      $(MAKECOOKIE)
+# 
+# install-scripts:
+#      install -d $(packageprefix)/$(LIBDIR)
+#      install -d $(packageprefix)/$(LIBDIR)/extras
+#      install -d $(packageprefix)/$(LIBDIR)/libraries
+#      install -d $(packageprefix)/$(LIBDIR)/settings
+#      install -d $(packageprefix)/$(LIBDIR)/tools
+#      install -d $(packageprefix)/bin
+#      for f in $(WORKSRC)/extras/*; do \
+#              install -m755 $$f $(packageprefix)/$(LIBDIR)/extras/`basename 
$$f`; \
+#              ln -s $(packagedir)/$(LIBDIR)/extras/`basename $$f` 
$(packageprefix)/bin/`basename $$f .py`; \
+#      done
+#      for f in $(WORKSRC)/tools/*; do \
+#              install -m755 $$f $(packageprefix)/$(LIBDIR)/tools/`basename 
$$f`; \
+#              ln -s $(packagedir)/$(LIBDIR)/tools/`basename $$f` 
$(packageprefix)/bin/`basename $$f .py`; \
+#      done
+#      for f in $(WORKSRC)/libraries/*; do \
+#              install -m644 $$f 
$(packageprefix)/$(LIBDIR)/libraries/`basename $$f`; \
+#      done
+#      install -m644 $(WORKSRC)/settings/defaults.ini 
$(packageprefix)/$(LIBDIR)/settings/defaults.ini
+#      $(MAKECOOKIE)

=== modified file 'pkg/bio/slimsuite/sha256sums'
--- a/pkg/bio/slimsuite/sha256sums      2016-06-17 19:57:40 +0000
+++ b/pkg/bio/slimsuite/sha256sums      2024-11-18 19:33:20 +0000
@@ -1,1 +1,1 @@
-eb972f3d3cb0bd9ab5399212bca17c63b401fdc886180afa1271ba1fe4a4ca83  
download/slimsuite.2014-08-25.tar.gz
+4ac70ad3d9dfda7741100873ff00cc617c96a1cb757ae092127706d329ec0c01  
download/v1.12.0.tar.gz