[med-svn] [Git][med-team/fasta3][master] 12 commits: routine-update: Add salsa-ci file
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Apr 18 11:00:50 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / fasta3
Commits:
4bfc3b1d by Michael R. Crusoe at 2020-04-18T08:23:14+02:00
routine-update: Add salsa-ci file
- - - - -
9e101912 by Michael R. Crusoe at 2020-04-18T08:23:16+02:00
routine-update: Rules-Requires-Root: no
- - - - -
bf7af42d by Michael R. Crusoe at 2020-04-18T08:23:16+02:00
debian/upstream/metadata: added Repository{,-Browse}
- - - - -
47336f89 by Michael R. Crusoe at 2020-04-18T08:23:40+02:00
Enable buildiing on non-X86 via SIMD Everywhere library
- - - - -
6d893da6 by Michael R. Crusoe at 2020-04-18T08:28:14+02:00
fasta3-doc: Multi-Arch: foreign
- - - - -
6d78f9b8 by Michael R. Crusoe at 2020-04-18T08:41:15+02:00
Enable cross building
- - - - -
1f42c7d5 by Michael R. Crusoe at 2020-04-18T08:44:54+02:00
Improve hardening
- - - - -
43917948 by Michael R. Crusoe at 2020-04-18T08:55:09+02:00
better cflags
- - - - -
396a298c by Michael R. Crusoe at 2020-04-18T09:22:38+02:00
test
- - - - -
7b206fef by Michael R. Crusoe at 2020-04-18T09:31:19+02:00
drop unneeded build-dep on zlib1g-dev
- - - - -
0ce7b226 by Michael R. Crusoe at 2020-04-18T09:40:50+02:00
Add autopkgtests
- - - - -
0ea65fc4 by Michael R. Crusoe at 2020-04-18T11:54:30+02:00
Install scripts/ to usr/share/fasta3/
- - - - -
15 changed files:
- − bin/README
- debian/changelog
- debian/control
- + debian/examples
- debian/fasta3.install
- debian/patches/Makefile.patch
- + debian/patches/adjust-scripts
- + debian/patches/local_tests
- debian/patches/series
- + debian/patches/simde
- debian/rules
- + debian/salsa-ci.yml
- + debian/tests/control
- + debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
bin/README deleted
=====================================
@@ -1 +0,0 @@
-Placeholder file to create destination for program binaries.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+fasta3 (36.3.8h.2020-02-11-3) unstable; urgency=medium
+
+ * Team upload.
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * debian/upstream/metadata: added Repository{,-Browse}
+ * Enable buildiing on non-X86 via SIMD Everywhere library
+ * fasta3-doc: Multi-Arch: foreign
+ * Enable cross building
+ * Improve hardening
+ * drop unneeded build-dep on zlib1g-dev
+ * Add autopkgtests
+ * Install scripts/ to usr/share/fasta3/
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 18 Apr 2020 11:46:22 +0200
+
fasta3 (36.3.8h.2020-02-11-2) unstable; urgency=medium
* Drop outdated README.source
=====================================
debian/control
=====================================
@@ -4,16 +4,28 @@ Uploaders: Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
- zlib1g-dev
+ libsimde-dev
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/fasta3
Vcs-Git: https://salsa.debian.org/med-team/fasta3.git
Homepage: https://fasta.bioch.virginia.edu
+Rules-Requires-Root: no
Package: fasta3
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
+Suggests: ${perl:Depends},
+ libdbi-perl,
+ libwww-perl,
+ libjson-perl,
+ libhtml-tableextract-perl,
+ libxml-twig-perl,
+ liburi-encode-perl,
+ libdbd-mysql-perl,
+ python3-mysqldb,
+ ncbi-blast+,
+ bedtools
Description: tools for searching collections of biological sequences
The FASTA programs find regions of local or global similarity between
Protein or DNA sequences, either by searching Protein or DNA databases,
@@ -60,9 +72,9 @@ Description: tools for searching collections of biological sequences
Package: fasta3-doc
Architecture: all
+Multi-Arch: foreign
Section: doc
-Depends: ${shlibs:Depends},
- ${misc:Depends}
+Depends: ${misc:Depends}
Breaks: fasta3 (<< 36.3.8h)
Replaces: fasta3 (<< 36.3.8h)
Description: user guide for FASTA tools
=====================================
debian/examples
=====================================
@@ -0,0 +1,2 @@
+seq/prot_test.lseg
+seq/mgstm1.aa
=====================================
debian/fasta3.install
=====================================
@@ -1 +1,2 @@
bin/[a-z]* usr/bin
+scripts/* usr/share/fasta3/
=====================================
debian/patches/Makefile.patch
=====================================
@@ -1,7 +1,25 @@
Description: Makefile
---- a/make/Makefile
-+++ b/make/Makefile
-@@ -34,6 +34,7 @@ THR_SUBS = pthr_subs2
+--- fasta3.orig/make/Makefile
++++ fasta3/make/Makefile
+@@ -5,7 +5,7 @@
+ # Dec 8, 2005 - with gcc4.0.2 (or .1) under Redhat Linux Fedora FC4 -03 breaks the alignment code
+ #
+
+-CC= gcc -g -O2
++CC ?= gcc -g -O2
+
+ #CC=gcc -Wall -pedantic -ansi -g -O
+ #CC = gcc -g -DDEBUG
+@@ -17,7 +17,7 @@
+ # this file works for x86 LINUX
+
+ # standard options
+-CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
++CFLAGS += -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
+ # -I/usr/local/include/mysql -DMYSQL_DB
+ #
+ #(for mySQL databases) (also requires change to Makefile34.common)
+@@ -34,6 +34,7 @@
THR_LIBS = -lpthread
THR_CC =
@@ -9,19 +27,19 @@ Description: Makefile
XDIR = /seqprg/bin
DROPGSW_NA_O = dropgsw2.o wm_align.o calcons_sw.o
---- a/make/Makefile.linux64_sse2
-+++ b/make/Makefile.linux64_sse2
+--- fasta3.orig/make/Makefile.linux64_sse2
++++ fasta3/make/Makefile.linux64_sse2
@@ -12,7 +12,8 @@
SHELL=/bin/bash
-CC = gcc -g -O -msse2
-+CC = gcc
-+CFLAGS = -g -O -msse2 $(CPPFLAGS)
++CC ?= gcc
++CFLAGS += -g -O $(CPPFLAGS)
LIB_DB=
#CC= gcc -pg -g -O -msse2 -ffast-math
-@@ -26,7 +27,7 @@ LIB_DB=
+@@ -26,7 +27,7 @@
# standard options
@@ -29,3 +47,121 @@ Description: Makefile
+CFLAGS += -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64
# -I/usr/include/mysql -DMYSQL_DB
# -DSUPERFAMNUM -DSFCHAR="'|'"
+
+--- fasta3.orig/make/Makefile.linux
++++ fasta3/make/Makefile.linux
+@@ -12,7 +12,7 @@
+
+ SHELL=/bin/bash
+
+-CC = gcc -g -O -msse2
++CC ?= gcc -g -O
+ LIB_DB=
+
+ #CC= gcc -pg -g -O -msse2 -ffast-math
+@@ -26,7 +26,7 @@
+
+ # standard options
+
+-CFLAGS= -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64
++CFLAGS += -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64
+ # -I/usr/include/mysql -DMYSQL_DB
+ # -DSUPERFAMNUM -DSFCHAR="'|'"
+
+--- fasta3.orig/make/Makefile.linux32
++++ fasta3/make/Makefile.linux32
+@@ -16,7 +16,7 @@
+ #LIB_DB=
+
+ #CC=gcc -Wall -pedantic -ansi -g -O
+-CC= /usr/local/parasoft/bin/insure -g -DDEBUG
++#CC= /usr/local/parasoft/bin/insure -g -DDEBUG
+ LIB_DB=-lz
+
+ # EBI uses the following with pgcc, -O3 does not work:
+@@ -25,7 +25,7 @@
+ # this file works for x86 LINUX
+
+ # standard options
+-CFLAGS= -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
++CFLAGS += -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
+ # -DSFCHAR="'|'" -dSUPERFAMNUM
+
+ # -I/usr/local/include/mysql -DMYSQL_DB
+--- fasta3.orig/make/Makefile.linux32_sse2
++++ fasta3/make/Makefile.linux32_sse2
+@@ -12,7 +12,7 @@
+
+ SHELL=/bin/bash
+
+-CC= gcc -g -O -msse2 -ffast-math
++CC ?= gcc -g -O
+ LIB_DB=
+ #CC = gcc -g -DDEBUG -msse2
+
+@@ -28,7 +28,7 @@
+
+ # standard options
+
+-CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP
++CFLAGS += -ffast-math -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP
+
+ # -DSUPERFAMNUM -DSFCHAR="'|'"
+
+--- fasta3.orig/make/Makefile.linux64
++++ fasta3/make/Makefile.linux64
+@@ -12,7 +12,7 @@
+
+ SHELL=/bin/bash
+
+-CC = gcc -g -O -msse2
++CC ?= gcc -g -O
+ LIB_DB=
+
+ #CC= gcc -pg -g -O -msse2 -ffast-math
+@@ -26,7 +26,7 @@
+
+ # standard options
+
+-CFLAGS= -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64
++CFLAGS += -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64
+ # -I/usr/include/mysql -DMYSQL_DB
+ # -DSUPERFAMNUM -DSFCHAR="'|'"
+
+@@ -38,13 +38,13 @@
+ # for mySQL databases
+ # LIB_M = -L/usr/lib64/mysql -lmysqlclient -lm
+
+-HFLAGS= -o
++HFLAGS= $(LDFLAGS) $(CPPFLAGS) -o
+ NFLAGS= -o
+
+ # for Linux
+ THR_SUBS = pthr_subs2
+ THR_LIBS = -lpthread
+-THR_CC =
++THR_CC = $(LDFLAGS) $(CPPFLAGS)
+
+ BIN = ../bin
+ XDIR = /seqprg/bin
+--- fasta3.orig/make/Makefile.pcom_t
++++ fasta3/make/Makefile.pcom_t
+@@ -171,14 +171,14 @@
+ $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB)
+
+ map_db : map_db.c uascii.h ncbl2_head.h
+- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++ $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) -o $(BIN)/map_db map_db.c
+
+ list_db : list_db.c
+- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++ $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) -o $(BIN)/list_db list_db.c
+
+
+ lav2ps : lav2plt.o lavplt_ps.o
+- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++ $(CC) $(LDFLAGS) $(CPPFLAGS) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+
+ lav2svg : lav2plt.o lavplt_svg.o
+- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
++ $(CC) $(LDFLAGS) $(CPPFLAGS) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
=====================================
debian/patches/adjust-scripts
=====================================
@@ -0,0 +1,560 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: adjust for installed use
+--- fasta3.orig/scripts/ann_exons_all.pl
++++ fasta3/scripts/ann_exons_all.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014,2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_exons_ens.pl
++++ fasta3/scripts/ann_exons_ens.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014,2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_exons_ncbi.pl
++++ fasta3/scripts/ann_exons_ncbi.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # ann_exons_ncbi.pl gets an annotation file from fasta36 -V with a line of the form:
+
+--- fasta3.orig/scripts/ann_exons_up_sql.pl
++++ fasta3/scripts/ann_exons_up_sql.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014,2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_exons_up_sql_www.pl
++++ fasta3/scripts/ann_exons_up_sql_www.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014,2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_exons_up_www.pl
++++ fasta3/scripts/ann_exons_up_www.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014,2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_feats2ipr.pl
++++ fasta3/scripts/ann_feats2ipr.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_feats2ipr_e.pl
++++ fasta3/scripts/ann_feats2ipr_e.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_feats_up_sql.pl
++++ fasta3/scripts/ann_feats_up_sql.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014,2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_feats_up_www2.pl
++++ fasta3/scripts/ann_feats_up_www2.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014,2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_ipr_www.pl
++++ fasta3/scripts/ann_ipr_www.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_pdb_cath.pl
++++ fasta3/scripts/ann_pdb_cath.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_pdb_vast.pl
++++ fasta3/scripts/ann_pdb_vast.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014, 2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_pfam30_tmptbl.pl
++++ fasta3/scripts/ann_pfam30_tmptbl.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014,2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_pfam_sql.pl
++++ fasta3/scripts/ann_pfam_sql.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_pfam_www.pl
++++ fasta3/scripts/ann_pfam_www.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014, 2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/ann_upfeats_pfam_www_e.pl
++++ fasta3/scripts/ann_upfeats_pfam_www_e.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/annot_blast_btop2.pl
++++ fasta3/scripts/annot_blast_btop2.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2017,2018 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/annot_blast_btop3.py
++++ fasta3/scripts/annot_blast_btop3.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+
+ ################################################################
+ # copyright (c) 2017,2018 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/annot_blast_btop4.py
++++ fasta3/scripts/annot_blast_btop4.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+
+ ################################################################
+ # copyright (c) 2017,2018 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/blastp_annot_cmd.sh
++++ fasta3/scripts/blastp_annot_cmd.sh
+@@ -55,14 +55,14 @@
+ # echo "OUTFILE = ${OUTNAME}"
+
+ #export BLAST_PATH="/ebi/extserv/bin/ncbi-blast+/bin"
+-export BLAST_PATH="/seqprg/bin"
++export BLAST_PATH="/usr/bin"
+
+ $BLAST_PATH/blastp -outfmt 11 $cmd > $bl_asn
+ $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 -html > $bl0_out
+ $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt '7 qseqid qlen sseqid slen pident length mismatch gapopen qstart qend sstart send evalue bitscore score btop' > $blt_out
+-annot_blast_btop2.pl --query $QUERY --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
++/usr/share/fasta3/annot_blast_btop2.pl --query $QUERY --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
+
+ ## rename_exons.py --have_qslen --dom_info $blt_ann > $blr_out
+-merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
++/usr/share/fasta3/merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
+
+ # $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 2 > $blm_out
+--- fasta3.orig/scripts/blastp_cmd.sh
++++ fasta3/scripts/blastp_cmd.sh
+@@ -22,7 +22,7 @@
+ # echo "OUTFILE = ${OUTNAME}"
+
+ #export BLAST_PATH="/ebi/extserv/bin/ncbi-blast+/bin"
+-export BLAST_PATH="/seqprg/bin"
++export BLAST_PATH="/usr/bin"
+
+ $BLAST_PATH/blastp -outfmt 11 $cmd > $bl_asn
+ $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 -html > $bl0_out
+--- fasta3.orig/scripts/exp_up_ensg.pl
++++ fasta3/scripts/exp_up_ensg.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2010, 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/expand_links.pl
++++ fasta3/scripts/expand_links.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2010, 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/expand_refseq_isoforms.pl
++++ fasta3/scripts/expand_refseq_isoforms.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2010, 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/expand_uniref50.pl
++++ fasta3/scripts/expand_uniref50.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2010, 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/expand_up_isoforms.pl
++++ fasta3/scripts/expand_up_isoforms.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2010, 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/fasta_annot_cmd.sh
++++ fasta3/scripts/fasta_annot_cmd.sh
+@@ -54,7 +54,7 @@
+ blt_out="$OUTNAME.fa_tab"
+ blr_out="$OUTNAME.fa_tab_rn"
+
+-export BLAST_PATH="/seqprg/bin"
++export BLAST_PATH="/usr/bin"
+ # BLAST_PATH="../bin"
+
+ cmd="$cmd -mF8CBL=$blt_out $QUERY $DATABASE"
+@@ -73,7 +73,7 @@
+ # run the program
+ $BLAST_PATH/$SRCH_CMD $cmd > $bl0_out
+
+-$BLAST_PATH/rename_exons.py --have_qslen --dom_info $blt_out > $blr_out
++/usr/share/fasta3/rename_exons.py --have_qslen --dom_info $blt_out > $blr_out
+
+ if [ ! -s $blr_out ]; then
+ # echo "# " `ls -l $blt_out $blr_out`
+@@ -81,4 +81,4 @@
+ # echo "# " `ls -l $blt_out $blr_out`
+ fi
+
+-$BLAST_PATH/merge_fasta_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
++/usr/share/fasta3/merge_fasta_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
+--- fasta3.orig/scripts/get_genome_seq.py
++++ fasta3/scripts/get_genome_seq.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+
+ ################
+ ## get_hg38_bed.py parses an HG38 coordinate into a pseudo-bed entry,
+--- fasta3.orig/scripts/get_protein.py
++++ fasta3/scripts/get_protein.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+
+ ## get_protein_www.py --
+ ## get a protein sequence from the Uniprot or NCBI/Refseq web sites using the accession
+--- fasta3.orig/scripts/get_protein_sql.py
++++ fasta3/scripts/get_protein_sql.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ ## get_protein_sql.py --
+ ## get a protein sequence from a local Uniprot or NCBI/Refseq mySQL database using the accession
+--- fasta3.orig/scripts/get_protein_sql_www.py
++++ fasta3/scripts/get_protein_sql_www.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+
+ ## get_protein.py --
+ ## get a protein sequence from Uniprot or NCBI/Refseq using the accession
+--- fasta3.orig/scripts/get_refseq.py
++++ fasta3/scripts/get_refseq.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+
+ import sys
+ import re
+--- fasta3.orig/scripts/get_uniprot.py
++++ fasta3/scripts/get_uniprot.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+
+ import sys
+ import re
+--- fasta3.orig/scripts/get_up_prot_iso_sql.py
++++ fasta3/scripts/get_up_prot_iso_sql.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+
+ import sys
+ import re
+--- fasta3.orig/scripts/lav2plt.pl
++++ fasta3/scripts/lav2plt.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # lav2plt.pl - produce plotfrom lav output */
+
+--- fasta3.orig/scripts/lavplt_ps.pl
++++ fasta3/scripts/lavplt_ps.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ #
+ ################################################################
+ # copyright (c) 2012, 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/lavplt_svg.pl
++++ fasta3/scripts/lavplt_svg.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ #
+ ################################################################
+ # copyright (c) 2012, 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/links2sql.pl
++++ fasta3/scripts/links2sql.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/m8_btop_msa.pl
++++ fasta3/scripts/m8_btop_msa.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014,2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/m9B_btop_msa.pl
++++ fasta3/scripts/m9B_btop_msa.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014,2015 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/map_exon_coords.py
++++ fasta3/scripts/map_exon_coords.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+ #
+ # given a -m8CB file with exon annotations for the query and subject,
+ # provide a function that maps subject coordinates to query, or vice versa
+--- fasta3.orig/scripts/merge_blast_btab.pl
++++ fasta3/scripts/merge_blast_btab.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2018 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/merge_fasta_btab.pl
++++ fasta3/scripts/merge_fasta_btab.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2018 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/relabel_domains.py
++++ fasta3/scripts/relabel_domains.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+
+ # Given a blast_tabular file with search results from one or more protein queries
+ #
+--- fasta3.orig/scripts/rename_exons.py
++++ fasta3/scripts/rename_exons.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python3
++#!/usr/bin/python3
+ #
+ # given a -m8CB file with exon annotations for the query and subject,
+ # adjust the subject exon names to match the query exon names
+--- fasta3.orig/scripts/summ_domain_ident.pl
++++ fasta3/scripts/summ_domain_ident.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ ################################################################
+ # copyright (c) 2014 by William R. Pearson and The Rector &
+--- fasta3.orig/scripts/test_py.sh
++++ fasta3/scripts/test_py.sh
+@@ -5,57 +5,58 @@
+ ## test python scripts
+ ##
+
+-echo 'get_genome_seq.py'
+-get_genome_seq.py chr1:109687874-109687909
++#echo 'get_genome_seq.py'
++#/usr/share/fasta3/get_genome_seq.py chr1:109687874-109687909
+
+ echo 'get_protein.py'
+-get_protein.py 'sp|P09488|GSTM1_HUMAN'
+-get_protein.py 'P09488'
+-get_protein.py 'NP_000552'
++#/usr/share/fasta3/get_protein.py 'sp|P09488|GSTM1_HUMAN'
++#/usr/share/fasta3/get_protein.py 'P09488'
++/usr/share/fasta3/get_protein.py 'NP_000552'
+
+ echo '################################################################'
+ echo 'requires mysql database'
+ echo 'get_protein_sql.py'
+-get_protein_sql.py 'sp|P09488|GSTM1_HUMAN'
+-get_protein_sql.py 'P09488'
+-get_protein_sql.py 'NP_000552'
++/usr/share/fasta3/get_protein_sql.py 'sp|P09488|GSTM1_HUMAN'
++/usr/share/fasta3/get_protein_sql.py 'P09488'
++/usr/share/fasta3/get_protein_sql.py 'NP_000552'
+
+ echo 'get_protein_sql_www.py'
+-get_protein_sql_www.py 'sp|P09488|GSTM1_HUMAN'
+-get_protein_sql_www.py 'P09488'
+-get_protein_sql_www.py 'NP_000552'
++/usr/share/fasta3/get_protein_sql_www.py 'sp|P09488|GSTM1_HUMAN'
++/usr/share/fasta3/get_protein_sql_www.py 'P09488'
++/usr/share/fasta3/get_protein_sql_www.py 'NP_000552'
+
+ echo 'get_refseq.py'
+-get_refseq.py NP_000552
+-get_refseq.py NP_0000552
++/usr/share/fasta3/get_refseq.py NP_000552
++/usr/share/fasta3/get_refseq.py NP_0000552
+
+-echo 'get_uniprot.py'
+-get_uniprot.py P09488
+-get_uniprot.py 'sp|P09488|GSTM1_HUMAN'
++# SSL error
++# echo 'get_uniprot.py'
++# /usr/share/fasta3/get_uniprot.py P09488
++# /usr/share/fasta3/get_uniprot.py 'sp|P09488|GSTM1_HUMAN'
+
+ echo '################################################################'
+ echo 'requires mysql database'
+ echo 'get_up_prot_iso_sql.py'
+-get_up_prot_iso_sql.py 'sp|P09488|GSTM1_HUMAN'
+-get_up_prot_iso_sql.py P09488
++/usr/share/fasta3/get_up_prot_iso_sql.py 'sp|P09488|GSTM1_HUMAN'
++/usr/share/fasta3/get_up_prot_iso_sql.py P09488
+
+-echo '################################################################'
+-echo 'map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output'
++# echo '################################################################'
++# echo 'map_exon_coords.py -- look for chrA:start-stop::chrB:start-stop in output'
+ # (a) produce an appropriate alignment file
+-fasta36 -q -m 8CBL -V \!ann_exons_up_sql.pl+--gen_coord+--exon_label -V q\!ann_exons_up_sql.pl+--gen_coord+--exon_label \!get_protein.py+P30711 \!get_protein.py+P20135 > hum_chk_map_test.m8CBL
++#fasta36 -q -m 8CBL -V \!/usr/share/fasta3/ann_exons_up_sql.pl+--gen_coord+--exon_label -V q\!/usr/share/fasta3/ann_exons_up_sql.pl+--gen_coord+--exon_label \!/usr/share/fasta3/get_protein.py+P30711 \!/usr/share/fasta3/get_protein.py+P20135 > hum_chk_map_test.m8CBL
+ # (b) expand chromosome locations on subject and query exons to both genomes
+-map_exon_coords.py hum_chk_map_test.m8CBL
++# /usr/share/fasta3/map_exon_coords.py hum_chk_map_test.m8CBL
+
+-echo 'rename_exons.py -- look for exon_X in output'
+-rename_exons.py hum_chk_map_test.m8CBL # produces a renamed exon_x
++# echo 'rename_exons.py -- look for exon_X in output'
++# /usr/share/fasta3/rename_exons.py hum_chk_map_test.m8CBL # produces a renamed exon_x
+
+-echo '################################################################'
+-echo 'annot_blast_btop4.py -- put annotations on blast BTOP alignment with (or without) raw_score'
+-# (a) from FASTA -m8CBl -- no raw score
+-echo '.fa_tab no raw score'
+-annot_blast_btop4.py --no_raw_score --have_qslen --query ../seq/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_file a1zb72_drome.annot mgstm1_v_a1zb72_dr.fa_tab
+-
+-## .bl_tab uses --ann_script because of multiple HSPs
+-echo '.bl_tab yes raw score'
+-annot_blast_btop4.py --raw_score --have_qslen --query ../seq/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_script ann_pfam_sql.pl mgstm1_v_a1zb72.bl_tab
++# echo '################################################################'
++# echo 'annot_blast_btop4.py -- put annotations on blast BTOP alignment with (or without) raw_score'
++# # (a) from FASTA -m8CBl -- no raw score
++# echo '.fa_tab no raw score'
++# /usr/share/fasta3/annot_blast_btop4.py --no_raw_score --have_qslen --query /usr/share/doc/fasta3/examples/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_file a1zb72_drome.annot mgstm1_v_a1zb72_dr.fa_tab
++#
++# ## .bl_tab uses --ann_script because of multiple HSPs
++# echo '.bl_tab yes raw score'
++# /usr/share/fasta3/annot_blast_btop4.py --raw_score --have_qslen --query /usr/share/doc/fasta3/examples/mgstm1.aa --q_ann_file gstm1_mouse.annot --ann_script ann_pfam_sql.pl mgstm1_v_a1zb72.bl_tab
+
+--- fasta3.orig/scripts/test_ann_scripts.sh
++++ fasta3/scripts/test_ann_scripts.sh
+@@ -9,22 +9,22 @@
+ # SP:GSTM1_HUMAN -- ebi searches without accession
+ ##
+
+-if [ ! $1=='' ]; then
++if [ ! "$1" = '' ]; then
+ script_file=$1
+ else
+- script_file=ann_script_list
++ script_file=/usr/share/fasta3/ann_script_list
+ fi
+
+-if [ ! $1=='' ]; then
++if [ ! "$1" = '' ]; then
+ ex_file=$1
+ else
+- ex_file=acc_examples
++ ex_file=/usr/share/fasta3/acc_examples
+ fi
+
+-for script in `cat $script_file `; do
+- for acc_type in `cat $ex_file`; do
+- echo $script ${acc_type}
+- $script ${acc_type}
+- done
+- echo '***DONE***' $script `date`
+-done
++while read -r script ; do
++ while read -r acc_type ; do
++ echo "${script}" "${acc_type}"
++ "${script}" "${acc_type}"
++ done < ${ex_file}
++ echo '***DONE***' "$script" "$(date)"
++done < ${script_file}
+--- fasta3.orig/scripts/ann_script_list
++++ fasta3/scripts/ann_script_list
+@@ -1,9 +1,7 @@
+-ann_exons_up_sql.pl
+-ann_exons_up_www.pl
+-ann_feats2ipr.pl
+-ann_feats_up_sql.pl
+-ann_feats_up_www2.pl
+-ann_ipr_www.pl
+-ann_pfam30.pl
+-ann_pfam_www.pl
+-ann_upfeats_pfam_www_e.pl
++/usr/share/fasta3/ann_exons_up_sql.pl
++/usr/share/fasta3/ann_exons_up_www.pl
++/usr/share/fasta3/ann_feats2ipr.pl
++/usr/share/fasta3/ann_feats_up_sql.pl
++/usr/share/fasta3/ann_feats_up_www2.pl
++/usr/share/fasta3/ann_ipr_www.pl
++/usr/share/fasta3/ann_upfeats_pfam_www_e.pl
=====================================
debian/patches/local_tests
=====================================
@@ -0,0 +1,262 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: disable tests that require external databases
+--- fasta3.orig/test/test.sh
++++ fasta3/test/test.sh
+@@ -7,71 +7,71 @@
+ mkdir results
+ fi
+
+-export FA_DB=/slib2/fa_dbs/qfo20.lseg
+-
+-echo "starting fasta36 - protein" `date`
+-../bin/fasta36 -q -m 6 -Z 100000 ../seq/mgstm1.aa:1-100 $FA_DB > results/test_m1.ok2.html
+-../bin/fasta36 -S -q -z 11 -O results/test_m1.ok2_p25 -s P250 ../seq/mgstm1.aa:100-218 $FA_DB
+-echo "done"
+-echo "starting fastxy36" `date`
+-../bin/fastx36 -m 9c -S -q ../seq/mgtt2_x.seq $FA_DB 1 > results/test_t2.xk1
+-../bin/fasty36 -S -q ../seq/mgtt2_x.seq $FA_DB > results/test_t2.yk2
+-../bin/fastx36 -m 9c -S -q -z 2 ../seq/mgstm1.esq $FA_DB > results/test_m1.xk2z2
+-../bin/fasty36 -S -q -z 2 ../seq/mgstm1.esq $FA_DB > results/test_m1.yk2z2
+-echo "done"
+-echo "starting fastxy36 rev" `date`
+-../bin/fastx36 -m 9c -q -m 5 ../seq/mgstm1.rev $FA_DB > results/test_m1.xk2r
+-../bin/fasty36 -q -m 5 -M 200-300 -z 2 ../seq/mgstm1.rev $FA_DB > results/test_m1.yk2rz2
+-../bin/fasty36 -q -m 5 -z 11 ../seq/mgstm1.rev $FA_DB > results/test_m1.yk2rz11
+-echo "done"
+-echo "starting ssearch36" `date`
+-../bin/ssearch36 -m 9c -S -z 3 -q ../seq/mgstm1.aa $FA_DB > results/test_m1.ssz3
+-../bin/ssearch36 -q -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa $FA_DB > results/test_m1.ss_p25
+-echo "done"
+-if [ -e ../bin/ssearch36s ]; then
+- echo "starting ssearch36s" `date`
+- ../bin/ssearch36s -m 9c -S -z 3 -q ../seq/mgstm1.aa $FA_DB > results/test_m1.sssz3
+- ../bin/ssearch36s -q -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa $FA_DB > results/test_m1.sss_p25
+- echo "done"
+-fi
++# export FA_DB=/slib2/fa_dbs/qfo20.lseg
++#
++# echo "starting fasta36 - protein" `date`
++# ../bin/fasta36 -q -m 6 -Z 100000 ../seq/mgstm1.aa:1-100 $FA_DB > results/test_m1.ok2.html
++# ../bin/fasta36 -S -q -z 11 -O results/test_m1.ok2_p25 -s P250 ../seq/mgstm1.aa:100-218 $FA_DB
++# echo "done"
++# echo "starting fastxy36" `date`
++# ../bin/fastx36 -m 9c -S -q ../seq/mgtt2_x.seq $FA_DB 1 > results/test_t2.xk1
++# ../bin/fasty36 -S -q ../seq/mgtt2_x.seq $FA_DB > results/test_t2.yk2
++# ../bin/fastx36 -m 9c -S -q -z 2 ../seq/mgstm1.esq $FA_DB > results/test_m1.xk2z2
++# ../bin/fasty36 -S -q -z 2 ../seq/mgstm1.esq $FA_DB > results/test_m1.yk2z2
++# echo "done"
++# echo "starting fastxy36 rev" `date`
++# ../bin/fastx36 -m 9c -q -m 5 ../seq/mgstm1.rev $FA_DB > results/test_m1.xk2r
++# ../bin/fasty36 -q -m 5 -M 200-300 -z 2 ../seq/mgstm1.rev $FA_DB > results/test_m1.yk2rz2
++# ../bin/fasty36 -q -m 5 -z 11 ../seq/mgstm1.rev $FA_DB > results/test_m1.yk2rz11
++# echo "done"
++# echo "starting ssearch36" `date`
++# ../bin/ssearch36 -m 9c -S -z 3 -q ../seq/mgstm1.aa $FA_DB > results/test_m1.ssz3
++# ../bin/ssearch36 -q -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa $FA_DB > results/test_m1.ss_p25
++# echo "done"
++# if [ -e ../bin/ssearch36s ]; then
++# echo "starting ssearch36s" `date`
++# ../bin/ssearch36s -m 9c -S -z 3 -q ../seq/mgstm1.aa $FA_DB > results/test_m1.sssz3
++# ../bin/ssearch36s -q -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa $FA_DB > results/test_m1.sss_p25
++# echo "done"
++# fi
+ echo "starting prss36(ssearch/fastx)" `date`
+ ../bin/ssearch36 -q -k 1000 -a ../seq/mgstm1.aa ../seq/xurt8c.aa > results/test_m1.rss
+ ../bin/fastx36 -q -k 1000 ../seq/mgstm1.esq ../seq/xurt8c.aa > results/test_m1.rfx
+ echo "done"
+-echo "starting ggsearch36/glsearch36" `date`
+-../bin/ggsearch36 -q -m 9i -w 80 ../seq/hahu.aa $FA_DB > results/test_h1.gg
+-../bin/glsearch36 -q -m 9i -w 80 ../seq/hahu.aa $FA_DB > results/test_h1.gl
+-../bin/ggsearch36 -q ../seq/gtt1_drome.aa $FA_DB > results/test_t1.gg
+-../bin/glsearch36 -q ../seq/gtt1_drome.aa $FA_DB > results/test_t1.gl
+-echo "done"
+-echo "starting fasta36 - DNA" `date`
+-../bin/fasta36 -S -q ../seq/mgstm1.nt %RMB 4 > results/test_m1.ok4
+-../bin/fasta36 -S -q ../seq/mgstm1.rev %RMB 4 > results/test_m1.ok4r
+-echo "done"
++# echo "starting ggsearch36/glsearch36" `date`
++# ../bin/ggsearch36 -q -m 9i -w 80 ../seq/hahu.aa $FA_DB > results/test_h1.gg
++# ../bin/glsearch36 -q -m 9i -w 80 ../seq/hahu.aa $FA_DB > results/test_h1.gl
++# ../bin/ggsearch36 -q ../seq/gtt1_drome.aa $FA_DB > results/test_t1.gg
++# ../bin/glsearch36 -q ../seq/gtt1_drome.aa $FA_DB > results/test_t1.gl
++# echo "done"
++# echo "starting fasta36 - DNA" `date`
++# ../bin/fasta36 -S -q ../seq/mgstm1.nt %RMB 4 > results/test_m1.ok4
++# ../bin/fasta36 -S -q ../seq/mgstm1.rev %RMB 4 > results/test_m1.ok4r
++# echo "done"
+ #echo "starting tfasta36" `date`
+ #tfasta36 -q ../seq/mgstm1.aa %RMB > results/test_m1.tk2
+ #echo "done"
+-echo "starting tfastxy36" `date`
+-../bin/tfastx36 -m 9c -q -i -3 -m 6 ../seq/mgstm1.aa %p > results/test_m1.tx2.html
+-../bin/tfasty36 -q -i -3 -N 5000 ../seq/mgstm1.aa %p > results/test_m1.ty2
+-echo "done"
+-echo "starting fastf36" `date`
+-../bin/fastf36 -q ../seq/m1r.aa $FA_DB > results/test_mf.ff
+-../bin/fastf36 -q ../seq/m1r.aa $FA_DB > results/test_mf.ff_s
+-echo "done"
+-echo "starting tfastf36" `date`
+-../bin/tfastf36 -q ../seq/m1r.aa %r > results/test_mf.tfr
+-echo "done"
+-echo "starting fasts36" `date`
+-../bin/fasts36 -q -V '*?@' ../seq/ngts.aa $FA_DB > results/test_m1.fs1
+-../bin/fasts36 -q ../seq/ngt.aa $FA_DB > results/test_m1.fs
+-../bin/fasts36 -q -n ../seq/mgstm1.nts m > results/test_m1.nfs
+-echo "starting fastm36" `date`
+-../bin/fastm36 -q ../seq/ngts.aa $FA_DB > results/test_m1.fm
+-../bin/fastm36 -q -n ../seq/mgstm1.nts m > results/test_m1.nfm
+-echo "done"
+-echo "starting tfasts36" `date`
+-../bin/tfasts36 -q ../seq/n0.aa %r > results/test_m1.ts_r
++# echo "starting tfastxy36" `date`
++# ../bin/tfastx36 -m 9c -q -i -3 -m 6 ../seq/mgstm1.aa %p > results/test_m1.tx2.html
++# ../bin/tfasty36 -q -i -3 -N 5000 ../seq/mgstm1.aa %p > results/test_m1.ty2
++# echo "done"
++# echo "starting fastf36" `date`
++# ../bin/fastf36 -q ../seq/m1r.aa $FA_DB > results/test_mf.ff
++# ../bin/fastf36 -q ../seq/m1r.aa $FA_DB > results/test_mf.ff_s
++# echo "done"
++# echo "starting tfastf36" `date`
++# ../bin/tfastf36 -q ../seq/m1r.aa %r > results/test_mf.tfr
++# echo "done"
++# echo "starting fasts36" `date`
++# ../bin/fasts36 -q -V '*?@' ../seq/ngts.aa $FA_DB > results/test_m1.fs1
++# ../bin/fasts36 -q ../seq/ngt.aa $FA_DB > results/test_m1.fs
++# ../bin/fasts36 -q -n ../seq/mgstm1.nts m > results/test_m1.nfs
++# echo "starting fastm36" `date`
++# ../bin/fastm36 -q ../seq/ngts.aa $FA_DB > results/test_m1.fm
++# ../bin/fastm36 -q -n ../seq/mgstm1.nts m > results/test_m1.nfm
++# echo "done"
++# echo "starting tfasts36" `date`
++# ../bin/tfasts36 -q ../seq/n0.aa %r > results/test_m1.ts_r
+ echo "starting lalign36" `date`
+ ../bin/lalign36 -k 1000 -q ../seq/mchu.aa ../seq/mchu.aa > results/test_mc.lal
+ ../bin/lalign36 -z 3 -q ../seq/mchu.aa ../seq/mchu.aa > results/test_mc.lal_z3
+--- fasta3.orig/test/test2G.sh
++++ fasta3/test/test2G.sh
+@@ -6,69 +6,69 @@
+ if [ ! -d results ]; then
+ mkdir results
+ fi
+-echo "starting fasta36 - protein" `date`
+-../bin/fasta36 -XM2G -q -m 6 -Z 100000 ../seq/mgstm1.aa:1-100 q > results/test2G_m1.ok2.html
+-../bin/fasta36 -q -XM2G -S -z 11 -O results/test2G_m1.ok2_p25 -s P250 ../seq/mgstm1.aa:100-218 q
+-echo "done"
+-echo "starting fastxy36" `date`
+-../bin/fastx36 -q -XM2G -m 9c -S ../seq/mgtt2_x.seq q 1 > results/test2G_t2.xk1
+-../bin/fasty36 -q -XM2G -S ../seq/mgtt2_x.seq q > results/test2G_t2.yk2
+-../bin/fastx36 -q -XM2G -m 9c -S -z 2 ../seq/mgstm1.esq a > results/test2G_m1.xk2z2
+-../bin/fasty36 -q -XM2G -S -z 2 ../seq/mgstm1.esq a > results/test2G_m1.yk2z2
+-echo "done"
+-echo "starting fastxy36 rev" `date`
+-../bin/fastx36 -q -XM2G -m 9c -m 5 ../seq/mgstm1.rev q > results/test2G_m1.xk2r
+-../bin/fasty36 -q -XM2G -m 5 -M 200-300 -z 2 ../seq/mgstm1.rev q > results/test2G_m1.yk2rz2
+-../bin/fasty36 -q -XM2G -m 5 -z 11 ../seq/mgstm1.rev q > results/test2G_m1.yk2rz11
+-echo "done"
+-echo "starting ssearch36" `date`
+-../bin/ssearch36 -q -XM2G -m 9c -S -z 3 ../seq/mgstm1.aa q > results/test2G_m1.ssz3
+-../bin/ssearch36 -q -XM2G -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa q > results/test2G_m1.ss_p25
+-echo "done"
+-if [ -e ../bin/ssearch36s ]; then
+- echo "starting ssearch36s" `date`
+- ../bin/ssearch36s -q -XM2G -m 9c -S -z 3 ../seq/mgstm1.aa q > results/test2G_m1.sssz3
+- ../bin/ssearch36s -q -XM2G -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa q > results/test2G_m1.sss_p25
+- echo "done"
+-fi
++# echo "starting fasta36 - protein" `date`
++# ../bin/fasta36 -XM2G -q -m 6 -Z 100000 ../seq/mgstm1.aa:1-100 q > results/test2G_m1.ok2.html
++# ../bin/fasta36 -q -XM2G -S -z 11 -O results/test2G_m1.ok2_p25 -s P250 ../seq/mgstm1.aa:100-218 q
++# echo "done"
++# echo "starting fastxy36" `date`
++# ../bin/fastx36 -q -XM2G -m 9c -S ../seq/mgtt2_x.seq q 1 > results/test2G_t2.xk1
++# ../bin/fasty36 -q -XM2G -S ../seq/mgtt2_x.seq q > results/test2G_t2.yk2
++# ../bin/fastx36 -q -XM2G -m 9c -S -z 2 ../seq/mgstm1.esq a > results/test2G_m1.xk2z2
++# ../bin/fasty36 -q -XM2G -S -z 2 ../seq/mgstm1.esq a > results/test2G_m1.yk2z2
++# echo "done"
++# echo "starting fastxy36 rev" `date`
++# ../bin/fastx36 -q -XM2G -m 9c -m 5 ../seq/mgstm1.rev q > results/test2G_m1.xk2r
++# ../bin/fasty36 -q -XM2G -m 5 -M 200-300 -z 2 ../seq/mgstm1.rev q > results/test2G_m1.yk2rz2
++# ../bin/fasty36 -q -XM2G -m 5 -z 11 ../seq/mgstm1.rev q > results/test2G_m1.yk2rz11
++# echo "done"
++# echo "starting ssearch36" `date`
++# ../bin/ssearch36 -q -XM2G -m 9c -S -z 3 ../seq/mgstm1.aa q > results/test2G_m1.ssz3
++# ../bin/ssearch36 -q -XM2G -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa q > results/test2G_m1.ss_p25
++# echo "done"
++# if [ -e ../bin/ssearch36s ]; then
++# echo "starting ssearch36s" `date`
++# ../bin/ssearch36s -q -XM2G -m 9c -S -z 3 ../seq/mgstm1.aa q > results/test2G_m1.sssz3
++# ../bin/ssearch36s -q -XM2G -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa q > results/test2G_m1.sss_p25
++# echo "done"
++# fi
+ echo "starting prss36(ssearch/fastx)" `date`
+ ../bin/ssearch36 -q -XM2G -k 1000 -a ../seq/mgstm1.aa ../seq/xurt8c.aa > results/test2G_m1.rss
+ ../bin/fastx36 -q -XM2G -k 1000 ../seq/mgstm1.esq ../seq/xurt8c.aa > results/test2G_m1.rfx
+ echo "done"
+-echo "starting ggsearch36/glsearch36" `date`
+-../bin/ggsearch36 -q -XM2G -m 9i -w 80 ../seq/hahu.aa q > results/test2G_h1.gg
+-../bin/glsearch36 -q -XM2G -m 9i -w 80 ../seq/hahu.aa q > results/test2G_h1.gl
+-../bin/ggsearch36 -q -XM2G ../seq/gtt1_drome.aa q > results/test2G_t1.gg
+-../bin/glsearch36 -q -XM2G ../seq/gtt1_drome.aa q > results/test2G_t1.gl
+-echo "done"
+-echo "starting fasta36 - DNA" `date`
+-../bin/fasta36 -S -q -XM2G ../seq/mgstm1.nt %RMB 4 > results/test2G_m1.ok4
+-../bin/fasta36 -S -q -XM2G ../seq/mgstm1.rev %RMB 4 > results/test2G_m1.ok4r
+-echo "done"
++# echo "starting ggsearch36/glsearch36" `date`
++# ../bin/ggsearch36 -q -XM2G -m 9i -w 80 ../seq/hahu.aa q > results/test2G_h1.gg
++# ../bin/glsearch36 -q -XM2G -m 9i -w 80 ../seq/hahu.aa q > results/test2G_h1.gl
++# ../bin/ggsearch36 -q -XM2G ../seq/gtt1_drome.aa q > results/test2G_t1.gg
++# ../bin/glsearch36 -q -XM2G ../seq/gtt1_drome.aa q > results/test2G_t1.gl
++# echo "done"
++# echo "starting fasta36 - DNA" `date`
++# ../bin/fasta36 -S -q -XM2G ../seq/mgstm1.nt %RMB 4 > results/test2G_m1.ok4
++# ../bin/fasta36 -S -q -XM2G ../seq/mgstm1.rev %RMB 4 > results/test2G_m1.ok4r
++# echo "done"
+ #echo "starting tfasta36" `date`
+ #tfasta36 -q -XM2G ../seq/mgstm1.aa %RMB > results/test2G_m1.tk2
+ #echo "done"
+-echo "starting tfastxy36" `date`
+-../bin/tfastx36 -m 9c -q -XM2G -i -3 -m 6 ../seq/mgstm1.aa %p > results/test2G_m1.tx2.html
+-../bin/tfasty36 -q -XM2G -i -3 -N 5000 ../seq/mgstm1.aa %p > results/test2G_m1.ty2
+-echo "done"
+-echo "starting fastf36" `date`
+-../bin/fastf36 -q -XM2G ../seq/m1r.aa q > results/test2G_mf.ff
+-../bin/fastf36 -q -XM2G ../seq/m1r.aa q > results/test2G_mf.ff_s
+-echo "done"
+-echo "starting tfastf36" `date`
+-../bin/tfastf36 -q -XM2G ../seq/m1r.aa %r > results/test2G_mf.tfr
+-echo "done"
+-echo "starting fasts36" `date`
+-../bin/fasts36 -q -XM2G -V '*?@' ../seq/ngts.aa q > results/test2G_m1.fs1
+-../bin/fasts36 -q -XM2G ../seq/ngt.aa q > results/test2G_m1.fs
+-../bin/fasts36 -q -XM2G -n ../seq/mgstm1.nts m > results/test2G_m1.nfs
+-echo "starting fastm36" `date`
+-../bin/fastm36 -q -XM2G ../seq/ngts.aa q > results/test2G_m1.fm
+-../bin/fastm36 -q -XM2G -n ../seq/mgstm1.nts m > results/test2G_m1.nfm
+-echo "done"
+-echo "starting tfasts36" `date`
+-../bin/tfasts36 -q -XM2G ../seq/n0.aa %r > results/test2G_m1.ts_r
++# echo "starting tfastxy36" `date`
++# ../bin/tfastx36 -m 9c -q -XM2G -i -3 -m 6 ../seq/mgstm1.aa %p > results/test2G_m1.tx2.html
++# ../bin/tfasty36 -q -XM2G -i -3 -N 5000 ../seq/mgstm1.aa %p > results/test2G_m1.ty2
++# echo "done"
++# echo "starting fastf36" `date`
++# ../bin/fastf36 -q -XM2G ../seq/m1r.aa q > results/test2G_mf.ff
++# ../bin/fastf36 -q -XM2G ../seq/m1r.aa q > results/test2G_mf.ff_s
++# echo "done"
++# echo "starting tfastf36" `date`
++# ../bin/tfastf36 -q -XM2G ../seq/m1r.aa %r > results/test2G_mf.tfr
++# echo "done"
++# echo "starting fasts36" `date`
++# ../bin/fasts36 -q -XM2G -V '*?@' ../seq/ngts.aa q > results/test2G_m1.fs1
++# ../bin/fasts36 -q -XM2G ../seq/ngt.aa q > results/test2G_m1.fs
++# ../bin/fasts36 -q -XM2G -n ../seq/mgstm1.nts m > results/test2G_m1.nfs
++# echo "starting fastm36" `date`
++# ../bin/fastm36 -q -XM2G ../seq/ngts.aa q > results/test2G_m1.fm
++# ../bin/fastm36 -q -XM2G -n ../seq/mgstm1.nts m > results/test2G_m1.nfm
++# echo "done"
++# echo "starting tfasts36" `date`
++# ../bin/tfasts36 -q -XM2G ../seq/n0.aa %r > results/test2G_m1.ts_r
+ echo "starting lalign36" `date`
+ ../bin/lalign36 -q -XM2G -k 1000 ../seq/mchu.aa ../seq/mchu.aa > results/test2G_mc.lal
+ ../bin/lalign36 -q -XM2G -z 3 ../seq/mchu.aa ../seq/mchu.aa > results/test2G_mc.lal_z3
=====================================
debian/patches/series
=====================================
@@ -1 +1,4 @@
Makefile.patch
+simde
+local_tests
+adjust-scripts
=====================================
debian/patches/simde
=====================================
@@ -0,0 +1,45 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: Fix compiling on non x86 with SIMD Everywhere
+
+diff --git a/src/global_sse2.c b/src/global_sse2.c
+index a5b2a3f..584bd67 100644
+--- a/src/global_sse2.c
++++ b/src/global_sse2.c
+@@ -19,7 +19,8 @@
+ #ifdef __SUNPRO_C
+ #include <sunmedia_intrin.h>
+ #else
+-#include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include "simde/x86/sse2.h"
+ #endif
+
+ #ifdef SW_SSE2
+diff --git a/src/glocal_sse2.c b/src/glocal_sse2.c
+index d2e8348..123d270 100644
+--- a/src/glocal_sse2.c
++++ b/src/glocal_sse2.c
+@@ -19,7 +19,8 @@
+ #ifdef __SUNPRO_C
+ #include <sunmedia_intrin.h>
+ #else
+-#include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include "simde/x86/sse2.h"
+ #endif
+
+ #ifdef SW_SSE2
+diff --git a/src/smith_waterman_sse2.c b/src/smith_waterman_sse2.c
+index d37f223..c638027 100644
+--- a/src/smith_waterman_sse2.c
++++ b/src/smith_waterman_sse2.c
+@@ -20,7 +20,8 @@
+ #ifdef __SUNPRO_C
+ #include <sunmedia_intrin.h>
+ #else
+-#include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include "simde/x86/sse2.h"
+ #endif
+
+ #ifdef SW_SSE2
=====================================
debian/rules
=====================================
@@ -13,19 +13,20 @@ MAKEFILE="../make/Makefile.linux64"
#endif
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-CFLAGS+=-flto
-LDFLAGS+=-flto
-
-# package maintainers to append CFLAGS
-#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
-# package maintainers to append LDFLAGS
-#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+export DEB_CFLAGS_MAINT_APPEND +=-flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd
+export DEB_LDFLAGS_MAINT_APPEND +=-flto
%:
- dh $@
+ dh $@ --sourcedirectory src
override_dh_auto_build:
- cd src && $(MAKE) -f $(MAKEFILE)
+ dh_auto_build --sourcedirectory make --builddirectory src --buildsystem makefile -- -f $(MAKEFILE)
+ # convoluted, but necessary to allow cross builds
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ cd test ; ./test2G.sh && ./test.sh && ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg
+endif
override_dh_auto_clean:
if [ -d src ]; then cd src && $(MAKE) -f $(MAKEFILE) clean-up; fi
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: fasta3, libdbi-perl, libwww-perl, libxml-twig-perl, libdbd-mysql-perl, libjson-perl, python3-mysqldb
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,21 @@
+#!/bin/bash
+set -ex
+
+pkg=fasta3
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # Double quote below to expand the temporary directory variable now versus
+ # later is on purpose.
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+/usr/share/fasta3/test_ann_scripts.sh
+/usr/share/fasta3/test_py.sh
+fasta36 -q mgstm1.aa prot_test.lseg
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Repository: https://github.com/wrpearson/fasta36.git
+Repository-Browse: https://github.com/wrpearson/fasta36
Bug-Database: https://github.com/wrpearson/fasta36/issues
Bug-Submit: https://github.com/wrpearson/fasta36/issues/new
Reference:
View it on GitLab: https://salsa.debian.org/med-team/fasta3/-/compare/4d6d2ae889c14d79aa01063bd7200bc13fdebfbc...0ea65fc4610e9fc91f33f7d1e959addc5fb68e54
--
View it on GitLab: https://salsa.debian.org/med-team/fasta3/-/compare/4d6d2ae889c14d79aa01063bd7200bc13fdebfbc...0ea65fc4610e9fc91f33f7d1e959addc5fb68e54
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