[med-svn] [Git][med-team/kalign][master] 11 commits: Add B-D on cmake
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sat Nov 5 18:48:20 GMT 2022
Nilesh Patra pushed to branch master at Debian Med / kalign
Commits:
3fddde20 by Nilesh Patra at 2022-11-05T22:52:01+05:30
Add B-D on cmake
- - - - -
e82cee6c by Nilesh Patra at 2022-11-05T22:53:59+05:30
Drop debian/patches/keep-debugging: debug flags are being passed now w/ cmake
- - - - -
0048da94 by Nilesh Patra at 2022-11-05T22:55:06+05:30
Drop debian/patches/no-native-build: no native build anymore
- - - - -
d276aafc by Nilesh Patra at 2022-11-05T22:55:40+05:30
Comment out simde patch for now, will re-enable
- - - - -
e6f7deeb by Nilesh Patra at 2022-11-05T23:27:00+05:30
d/rules: Update install/build location with prefixing it with obj-* since binary install loc change w/ cmake. Also remove timescorealn as this is no longer provided/install, change that with kalignfmt
- - - - -
4b9c7601 by Nilesh Patra at 2022-11-05T23:27:00+05:30
Remove manpage for timescorealn
- - - - -
d14982cb by Nilesh Patra at 2022-11-05T23:27:00+05:30
Update installing examples at right loc
- - - - -
d1c5a510 by Nilesh Patra at 2022-11-05T23:42:25+05:30
Update potential fallout
- - - - -
8f420c53 by Nilesh Patra at 2022-11-05T23:48:44+05:30
Let dh_auto_install do its job well, make custom changes on amd64 and i386 post that
- - - - -
0af2b088 by Nilesh Patra at 2022-11-05T18:41:41+00:00
Kalign no longer allows un-aligned seq to be re-formatted hence removing test 7 for now
- - - - -
96df07ad by Nilesh Patra at 2022-11-05T18:44:02+00:00
Add manpage for kalignfmt and update old manpage for kalign
- - - - -
11 changed files:
- debian/control
- debian/createmanpages
- debian/kalign.1
- debian/kalign.examples
- + debian/kalignfmt.1
- − debian/patches/keep-debugging
- − debian/patches/no-native-build
- debian/patches/series
- debian/rules
- debian/tests/run-unit-test
- − debian/timescorealn.1
Changes:
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Charles Plessy <plessy at debian.org>, Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 13), libsimde-dev
+Build-Depends: debhelper-compat (= 13), libsimde-dev, cmake
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/kalign
Vcs-Git: https://salsa.debian.org/med-team/kalign.git
=====================================
debian/createmanpages
=====================================
@@ -29,7 +29,7 @@ EOT
# If program name is different from package name or title should be
# different from package short description change this here
-progname=timescorealn
+progname=kalignfmt
help2man --no-info --no-discard-stderr --help-option="-h" \
--name="$NAME" \
--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
=====================================
debian/kalign.1
=====================================
@@ -1,19 +1,34 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH KALIGN "1" "August 2020" "kalign 3.2.3" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5.
+.TH KALIGN "1" "November 2022" "kalign 3.3.4" "User Commands"
.SH NAME
kalign \- Global and progressive multiple sequence alignment
.SH SYNOPSIS
.B kalign-avx2
\fI\,-i <seq file> -o <out aln>\/\fR
.SH DESCRIPTION
-Kalign (3.2.3)
+Kalign (3.3.4)
.SH OPTIONS
.TP
\fB\-\-format\fR
: Output format. [Fasta]
.TP
-\fB\-\-reformat\fR
-: Reformat existing alignment. [NA]
+\fB\-\-type\fR
+: Alignment type (rna, dna, internal). [rna]
+Options: protein, divergent (protein)
+.IP
+rna, dna, internal (nuc).
+.TP
+\fB\-\-gpo\fR
+: Gap open penalty. []
+.TP
+\fB\-\-gpe\fR
+: Gap extension penalty. []
+.TP
+\fB\-\-tgpe\fR
+: Terminal gap extension penalty. []
+.TP
+\fB\-n\fR/\-\-nthreads
+: Number of threads. [4]
.TP
\fB\-\-version\fR (\fB\-V\fR/\-v)
: Prints version. [NA]
@@ -26,7 +41,7 @@ Combining multiple input files:
.IP
kalign seqsA.fa seqsB.fa seqsC.fa \-f fasta > combined.afa
.SH COPYRIGHT
-Copyright \(co 2006,2019,2020 Timo Lassmann
+Copyright \(co 2006,2019,2020,2021 Timo Lassmann
.PP
This program comes with ABSOLUTELY NO WARRANTY; for details type:
`kalign \fB\-showw\fR'.
@@ -39,6 +54,4 @@ Lassmann, Timo.
"Kalign 3: multiple sequence alignment of large data sets."
Bioinformatics (2019)
https://doi.org/10.1093/bioinformatics/btz795
-.SH AUTHOR
- This manpage was written by Nilesh Patra for the Debian distribution and
- can be used for any other usage of the program.
+.SH AUTHOR\n This manpage was written by Nilesh Patra for the Debian distribution and\n can be used for any other usage of the program.
=====================================
debian/kalign.examples
=====================================
@@ -1,2 +1,2 @@
debian/tests/data/*
-dev/data/B*
+tests/data/B*
=====================================
debian/kalignfmt.1
=====================================
@@ -0,0 +1,51 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5.
+.TH KALIGNFMT "1" "November 2022" "kalignfmt 3.3.4" "User Commands"
+.SH NAME
+kalignfmt \- Global and progressive multiple sequence alignment
+.SH SYNOPSIS
+.B kalignfmt-avx2
+\fI\,-i <seq file> -o <out aln>\/\fR
+.SH DESCRIPTION
+Kalign (3.3.4)
+.SH OPTIONS
+.TP
+\fB\-\-format\fR
+: Output format. [Fasta]
+.TP
+\fB\-\-reformat\fR
+: Reformat existing alignment. [NA]
+.TP
+\fB\-\-changename\fR
+: Change sequence names to 1 .. N. [NA]
+.TP
+\fB\-\-unalign\fR
+: Remove gaps and write to fasta. [NA]
+.TP
+\fB\-\-clean\fR
+: Perform additional checks on alignment. [NA]
+.TP
+\fB\-\-version\fR (\fB\-V\fR/\-v)
+: Prints version. [NA]
+.SH EXAMPLES
+Passing sequences via stdin:
+.IP
+cat input.fa | kalign \-f fasta > out.afa
+.PP
+Combining multiple input files:
+.IP
+kalign seqsA.fa seqsB.fa seqsC.fa \-f fasta > combined.afa
+.SH COPYRIGHT
+Copyright \(co 2006,2019,2020,2021 Timo Lassmann
+.PP
+This program comes with ABSOLUTELY NO WARRANTY; for details type:
+`kalign \fB\-showw\fR'.
+.br
+This is free software, and you are welcome to redistribute it
+under certain conditions; consult the COPYING file for details.
+.SS "Please cite:"
+.IP
+Lassmann, Timo.
+"Kalign 3: multiple sequence alignment of large data sets."
+Bioinformatics (2019)
+https://doi.org/10.1093/bioinformatics/btz795
+.SH AUTHOR\n This manpage was written by Nilesh Patra for the Debian distribution and\n can be used for any other usage of the program.
=====================================
debian/patches/keep-debugging deleted
=====================================
@@ -1,14 +0,0 @@
-Author: Michael R. Crusoe <crusoe at debian.org>
-Description: don't filter out "-g" from CFLAGS
-
-So we can save the debugging symbols to the debug package
---- kalign.orig/m4/ax_set_compile_flags.m4
-+++ kalign/m4/ax_set_compile_flags.m4
-@@ -15,7 +15,6 @@
-
- changequote({,})
- CFLAGS=`echo "$CFLAGS" | $SED -e 's/-O[0-9s]*//g'`
-- CFLAGS=`echo "$CFLAGS" | $SED -e 's/-g[0-9]*//g'`
- changequote([,])
-
-
=====================================
debian/patches/no-native-build deleted
=====================================
@@ -1,20 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: Don't build with all the SIMD compiler flags
-
-This breaks the Debian baseline
---- kalign.orig/configure.ac
-+++ kalign/configure.ac
-@@ -17,13 +17,10 @@
-
- AC_CONFIG_MACRO_DIR([m4])
-
--m4_include([m4/ax_ext.m4])
- m4_include([m4/ax_valgrind_check.m4])
- m4_include([m4/ax_check_compile_flag.m4])
- m4_include([m4/ax_set_compile_flags.m4])
-
--AX_EXT
--
- AX_ENABLE_DEBUG
-
- AC_ARG_ENABLE(openmp, [AC_HELP_STRING([--enable-openmp],[use OpenMP directives for parallelism])], enable_openmp=$enableval, enable_openmp=no)
=====================================
debian/patches/series
=====================================
@@ -1,3 +1 @@
-simde
-no-native-build
-keep-debugging
+#simde
=====================================
debian/rules
=====================================
@@ -6,6 +6,7 @@ include /usr/share/dpkg/default.mk
export DEB_CFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
export DEB_CXXFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+OBJ_DIR=obj-$(DEB_HOST_GNU_TYPE)
prefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr
libexecdir=$(prefix)/lib/$(DEB_SOURCE)
@@ -19,27 +20,28 @@ override_dh_auto_build:
ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
mkdir -p $(prefix)
mkdir -p $(libexecdir)
- $(foreach SIMD,$(AMD64_SIMD_LEVELS), make clean ; dh_auto_configure -- CFLAGS="$(CFLAGS) -m$(SIMD)" && dh_auto_build && cp src/kalign src/kalign-$(SIMD) && cp src/timescorealn src/timescorealn-$(SIMD) && ) true
- make clean ; dh_auto_configure && dh_auto_build && \
- cp src/kalign src/kalign-plain && \
- cp src/timescorealn src/timescorealn-plain
+ $(foreach SIMD,$(AMD64_SIMD_LEVELS), make clean ; dh_auto_configure -- CFLAGS="$(CFLAGS) -m$(SIMD)" && dh_auto_build && cp $(OBJ_DIR)/src/kalign $(OBJ_DIR)/src/kalign-$(SIMD) && cp $(OBJ_DIR)/src/kalignfmt $(OBJ_DIR)/src/kalignfmt-$(SIMD) && ) true
+ $(MAKE) clean ; dh_auto_configure && dh_auto_build && \
+ cp $(OBJ_DIR)/src/kalign $(OBJ_DIR)/src/kalign-plain && \
+ cp $(OBJ_DIR)/src/kalignfmt $(OBJ_DIR)/src/kalignfmt-plain
ifeq (i386,$(DEB_HOST_ARCH))
- $(foreach SIMD,$(i386_SIMD_LEVELS), make clean ; dh_auto_configure -- CFLAGS="$(CFLAGS) -m$(SIMD)" && dh_auto_build && cp src/kalign src/kalign-$(SIMD) && cp src/timescorealn src/timescorealn-$(SIMD) && ) true
+ $(foreach SIMD,$(i386_SIMD_LEVELS), make clean ; dh_auto_configure -- CFLAGS="$(CFLAGS) -m$(SIMD)" && dh_auto_build && cp $(OBJ_DIR)/src/kalign $(OBJ_DIR)/src/kalign-$(SIMD) && cp $(OBJ_DIR)/src/kalignfmt $(OBJ_DIR)/src/kalignfmt-$(SIMD) && ) true
endif
else
dh_auto_build
endif
-override_dh_auto_install:
+override_dh_install:
ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
+ find debian/$(DEB_SOURCE)/usr/bin -type f -name kalign -delete
dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/
- dh_install src/kalign-* usr/lib/$(DEB_SOURCE)/
- dh_install src/timescorealn-* usr/lib/$(DEB_SOURCE)/
+ dh_install $(OBJ_DIR)/src/kalign-* usr/lib/$(DEB_SOURCE)/
+ dh_install $(OBJ_DIR)/src/kalignfmt-* usr/lib/$(DEB_SOURCE)/
mkdir -p $(prefix)/bin
cd $(prefix)/bin \
- && $(foreach PROG,kalign timescorealn,ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $(PROG) &&) true
+ && $(foreach PROG,kalign kalignfmt,ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $(PROG) &&) true
else
- dh_auto_install
+ dh_install
endif
override_dh_gencontrol:
=====================================
debian/tests/run-unit-test
=====================================
@@ -52,10 +52,4 @@ cat BB11001.msf | kalign -o out.afa
cat BB12006.msf | kalign -o out.afa
cat BB30014.msf | kalign -o out.afa
-echo TEST 7: Reformat existing alignment
-# kalign -i BB11001.msf -r afa -o out.afa
-cat BB11001.msf | kalign -r afa -o out.afa
-cat BB12006.msf | kalign -r afa -o out.afa
-cat BB30014.msf | kalign -r afa -o out.afa
-
echo "PASS"
=====================================
debian/timescorealn.1 deleted
=====================================
@@ -1,38 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
-.TH TIMESCOREALN "1" "August 2020" "timescorealn 3.2.3" "User Commands"
-.SH NAME
-timescorealn \- Global and progressive multiple sequence alignment
-.SH SYNOPSIS
-.B timescorealn-avx2
-[\fI\,-options\/\fR] \fI\,-test <test sequences> -ref <reference alignment> -program <kalign|clustalo|muscle> -o <outfile>\/\fR
-.SH DESCRIPTION
-[2020\-08\-04 21:41:11] : ERROR : No test file
-.IP
-(time_and_score_aln.c line 111)
-.PP
-NOTE: the program appends results to the output file.
-.SH OPTIONS
-.TP
-\fB\-\-scratch\fR
-: Scratch directory. [NA]
-.PP
-Usage: timescorealn\-avx2 [\-options] \fB\-test\fR <test sequences> \fB\-ref\fR <reference alignment> \fB\-program\fR <kalign|clustalo|muscle> \fB\-o\fR <outfile>
-.PP
-NOTE: the program appends results to the output file.
-.TP
-\fB\-\-scratch\fR
-: Scratch directory. [NA]
-.PP
-[2020\-08\-04 21:41:11] : WARNING : Something went wrong. Use this program like this:
-.IP
-(time_and_score_aln.c line 154)
-.PP
-Usage: timescorealn\-avx2 [\-options] \fB\-test\fR <test sequences> \fB\-ref\fR <reference alignment> \fB\-program\fR <kalign|clustalo|muscle> \fB\-o\fR <outfile>
-.PP
-NOTE: the program appends results to the output file.
-.TP
-\fB\-\-scratch\fR
-: Scratch directory. [NA]
-.SH AUTHOR
- This manpage was written by Nilesh Patra for the Debian distribution and
- can be used for any other usage of the program.
View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/28b6940a0058d8b759887209534f2a60a5a63a84...96df07adf285165e9a8c1159e47bc3713eec4ae1
--
View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/28b6940a0058d8b759887209534f2a60a5a63a84...96df07adf285165e9a8c1159e47bc3713eec4ae1
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