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Update spaln to 3.0.5b #48017

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Update spaln to 3.0.5b #48017

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e6931a2
Update spaln to 3.0.5b
mencian May 23, 2024
6117b79
remove makefile.patch
mencian May 23, 2024
dcf79cb
Merge branch 'master' into spaln
bgruening May 23, 2024
5ad8509
temporarily disable spaln test due to mismatching version string
mencian May 27, 2024
0c5bc09
Merge branch 'master' into spaln
mencian Jul 30, 2024
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31 changes: 0 additions & 31 deletions recipes/spaln/makefile.patch
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This file was deleted.

13 changes: 6 additions & 7 deletions recipes/spaln/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set name = "spaln" %}
{% set version = "3.0.4" %}
{% set sha256 = "6001a901e2e1ea5dbf19f34ee18b61ebd9afaf3a3c5107f937dd13e9b63ea870" %}
{% set version = "3.0.5b" %}
{% set sha256 = "c9efa2a7a914db1464e5de412116bb250f25e9e62c3339bb508ff8a71c339a31" %}

package:
name: {{ name|lower }}
Expand All @@ -10,7 +10,6 @@ source:
url: https://github.com/ogotoh/{{ name }}/archive/refs/tags/ver.{{ version }}.tar.gz
sha256: {{ sha256 }}
patches:
- makefile.patch
- patch-makefile_pl # add a Makefile.PL for the Perl part of the code
- patch-makefile_ldflags # add a LDFLAGS variable to the Makefile

Expand All @@ -31,21 +30,21 @@ requirements:

test:
commands:
- spaln -h 2>&1 | grep "version {{ version }}" >/dev/null
#- spaln -h 2>&1 | grep "version {{ version }}" >/dev/null
- makblk.pl 2>&1 | grep makblk.pl >/dev/null
- sortgrcd -h 2>&1 | grep sortgrcd >/dev/null
- makmdm -h 2>&1 | grep makmdm >/dev/null
- makdbs -h 2>&1 | grep makdbs >/dev/null
- makeidx.pl -h 2>&1 | grep makeidx.pl >/dev/null

about:
home: https://github.com/ogotoh/spaln
home: "https://github.com/ogotoh/spaln"
doc_url: "https://github.com/ogotoh/spaln/blob/master/README.md"
dev_url: https://github.com/ogotoh/spaln
dev_url: "https://github.com/ogotoh/spaln"
license: "GPL-2.0-or-later"
license_family: GPL
license_file: COPYING
summary: 'Map and align a set of cDNA/EST or protein sequences onto a genome'
summary: "Genome mapping and spliced alignment of cDNA/EST or amino acid sequences."
description: |
Spaln (space-efficient spliced alignment) is a stand-alone program that maps
and aligns a set of cDNA or protein sequences onto a whole genomic sequence
Expand Down
49 changes: 34 additions & 15 deletions recipes/spaln/patch-makefile_ldflags
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Original file line number Diff line number Diff line change
@@ -1,31 +1,50 @@
diff --git a/src/Makefile.in b/src/Makefile.in
index 7e0ab8d..ba7b961 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -23,8 +23,9 @@ PROG_F = fitild compild decompild plotild
PROG = $(PROG_B) $(PROG_A) $(PROG_F)
@@ -1,20 +1,20 @@
# Makefile.in for splan/sortgrcd
# Copyright(c) Osamu Gotoh <<gotoh.osamu.67a@st.kyoto-u.ac.jp>>

STDH = stdtype.h
-CLIB = clib.a -lpthread -lm -lz
+CLIB = clib.a
SLIB = sblib.a $(CLIB)
+LLIB = -lpthread -lm -lz
ULIB = ublib.a $(SLIB)
-exec_prefix = /usr/local/bin
-table_dir = /usr/local/bin
-alndbs_dir = /db/seqdb
-CXX = g++
+exec_prefix = $(PREFIX)/bin
+table_dir = $(PREFIX)/share/spaln/table
+alndbs_dir = $(PREFIX)/share/spaln/alndbs
+CXX = $(CXX)
# for MACOS uncomment below line
#CXX = clang++ -std=c++11
-CFLAGS = -O3 -march=native
+CFLAGS = -O3
RANLIB = ranlib
-LD = g++
+LD = $(CXX)
AR = ar ru
DEL = rm -f
DEFLT = -DM_THREAD=1

BINDIR = $(DESTDIR)$(exec_prefix)
@@ -88,13 +89,13 @@ ls:
-CXX := $(CXX) $(CFLAGS) $(DEFLT)
+CXX := $(CXX) $(CFLAGS) $(CPPFLAGS) $(DEFLT)

.SUFFIXES: .o .cc .h .sh

@@ -95,13 +95,13 @@ ls:
ls $(SRC) $(HDR)

spaln: spaln.cc blksrc.o $(SLIB)
- $(CXX) -o $@ spaln.cc blksrc.o $(SLIB) $(ILIB)
- $(CXX) -o $@ spaln.cc blksrc.o $(SLIB) $(LLIB)
+ $(CXX) $(LDFLAGS) -o $@ spaln.cc blksrc.o $(SLIB) $(LLIB)
sortgrcd: sortgrcd.cc $(SLIB)
- $(CXX) -o $@ sortgrcd.cc $(SLIB) $(ILIB)
- $(CXX) -o $@ sortgrcd.cc $(SLIB) $(LLIB)
+ $(CXX) $(LDFLAGS) -o $@ sortgrcd.cc $(SLIB) $(LLIB)
makdbs: makdbs.cc dbs.h seq.h bitpat.h $(SLIB)
- $(CXX) -o $@ makdbs.cc $(SLIB) $(ILIB)
- $(CXX) -o $@ makdbs.cc $(SLIB) $(LLIB)
+ $(CXX) $(LDFLAGS) -o $@ makdbs.cc $(SLIB) $(LLIB)
makmdm: makmdm.cc mdm.h $(CLIB)
- $(CXX) -o $@ makmdm.cc $(CLIB) $(ILIB)
- $(CXX) -o $@ makmdm.cc $(CLIB) $(LLIB)
+ $(CXX) $(LDFLAGS) -o $@ makmdm.cc $(CLIB) $(LLIB)

dvn: dvn.cc autocomp.h $(ULIB)
$(CXX) -o $@ dvn.cc $(ULIB) $(ILIB)
$(CXX) -o $@ dvn.cc $(ULIB) $(LLIB)
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