Commit 6a6d53643e0b704971911d662496a9d4c83ae652 - fasta3

Refresh patches Andreas Tille 1 year, 4 months ago

5 changed file(s) with 239 addition(s) and 494 deletion(s). Raw diff Collapse all Expand all

-158

debian/patches/Makefile.patch less more

0	0	Description: Makefile
1	1	Forwarded: https://github.com/wrpearson/fasta36/pull/24
2		--- fasta3.orig/make/Makefile
3		+++ fasta3/make/Makefile
4		@@ -5,7 +5,7 @@
5		# Dec 8, 2005 - with gcc4.0.2 (or .1) under Redhat Linux Fedora FC4 -03 breaks the alignment code
6		#
7
8		-CC= gcc -g -O2
9		+CC ?= gcc -g -O2
10
11		#CC=gcc -Wall -pedantic -ansi -g -O
12		#CC = gcc -g -DDEBUG
13		@@ -17,7 +17,7 @@
14		# this file works for x86 LINUX
15
16		# standard options
17		-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
18		+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
19		# -I/usr/local/include/mysql -DMYSQL_DB
20		#
21		#(for mySQL databases) (also requires change to Makefile34.common)
22		@@ -34,6 +34,7 @@
23		THR_LIBS = -lpthread
24		THR_CC =
25
26		+BIN = ../bin
27		XDIR = /seqprg/bin
28
29		DROPGSW_NA_O = dropgsw2.o wm_align.o calcons_sw.o
30		--- fasta3.orig/make/Makefile.linux64_sse2
31		+++ fasta3/make/Makefile.linux64_sse2
32		@@ -12,7 +12,8 @@
33
34		SHELL=/bin/bash
35
36		-CC = gcc -g -O -msse2
37		+CC ?= gcc
38		+CFLAGS += -g -O $(CPPFLAGS)
39		LIB_DB=
40
41		#CC= gcc -pg -g -O -msse2 -ffast-math
42		@@ -26,7 +27,7 @@
43
44		# standard options
45
46		-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
47		+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
48		# -I/usr/include/mysql -DMYSQL_DB
49		# -DSUPERFAMNUM -DSFCHAR="'\|'"
50
51		--- fasta3.orig/make/Makefile.linux
52		+++ fasta3/make/Makefile.linux
53		@@ -12,7 +12,7 @@
54
55		SHELL=/bin/bash
56
57		-CC = gcc -g -O -msse2
58		+CC ?= gcc -g -O
59		LIB_DB=
60
61		#CC= gcc -pg -g -O -msse2 -ffast-math
62		@@ -26,7 +26,7 @@
63
64		# standard options
65
66		-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
67		+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
68		# -I/usr/include/mysql -DMYSQL_DB
69		# -DSUPERFAMNUM -DSFCHAR="'\|'"
70
71		--- fasta3.orig/make/Makefile.linux32
72		+++ fasta3/make/Makefile.linux32
73		@@ -16,7 +16,7 @@
74		#LIB_DB=
75
76		#CC=gcc -Wall -pedantic -ansi -g -O
77		-CC= /usr/local/parasoft/bin/insure -g -DDEBUG
78		+#CC= /usr/local/parasoft/bin/insure -g -DDEBUG
79		LIB_DB=-lz
80
81		# EBI uses the following with pgcc, -O3 does not work:
82		@@ -25,7 +25,7 @@
	2	--- a/make/Makefile.linux32
	3	+++ b/make/Makefile.linux32
	4	@@ -25,7 +25,7 @@ LIB_DB=-lz
83	5	# this file works for x86 LINUX
84	6
85	7	# standard options

88	10	# -DSFCHAR="'\|'" -dSUPERFAMNUM
89	11
90	12	# -I/usr/local/include/mysql -DMYSQL_DB
91		--- fasta3.orig/make/Makefile.linux32_sse2
92		+++ fasta3/make/Makefile.linux32_sse2
93		@@ -12,7 +12,7 @@
94
95		SHELL=/bin/bash
96
97		-CC= gcc -g -O -msse2 -ffast-math
98		+CC ?= gcc -g -O
99		LIB_DB=
100		#CC = gcc -g -DDEBUG -msse2
101
102		@@ -28,7 +28,7 @@
103
104		# standard options
105
106		-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
107		+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
108
109		# -DSUPERFAMNUM -DSFCHAR="'\|'"
110
111		--- fasta3.orig/make/Makefile.linux64
112		+++ fasta3/make/Makefile.linux64
113		@@ -12,7 +12,7 @@
114
115		SHELL=/bin/bash
116
117		-CC = gcc -g -O -msse2
118		+CC ?= gcc -g -O
119		LIB_DB=
120
121		#CC= gcc -pg -g -O -msse2 -ffast-math
122		@@ -26,7 +26,7 @@
123
124		# standard options
125
126		-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
127		+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
128		# -I/usr/include/mysql -DMYSQL_DB
129		# -DSUPERFAMNUM -DSFCHAR="'\|'"
130
131		@@ -38,13 +38,13 @@
132		# for mySQL databases
133		# LIB_M = -L/usr/lib64/mysql -lmysqlclient -lm
134
135		-HFLAGS= -o
136		+HFLAGS= $(LDFLAGS) $(CPPFLAGS) -o
137		NFLAGS= -o
138
139		# for Linux
140		THR_SUBS = pthr_subs2
141		THR_LIBS = -lpthread
142		-THR_CC =
143		+THR_CC = $(LDFLAGS) $(CPPFLAGS)
144
145		BIN = ../bin
146		XDIR = /seqprg/bin
147		--- fasta3.orig/make/Makefile.pcom_t
148		+++ fasta3/make/Makefile.pcom_t
149		@@ -171,14 +171,14 @@
150		$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB)
151
152		map_db : map_db.c uascii.h ncbl2_head.h
153		- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
154		+ $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) -o $(BIN)/map_db map_db.c
155
156		list_db : list_db.c
157		- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
158		+ $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) -o $(BIN)/list_db list_db.c
159
160
161		lav2ps : lav2plt.o lavplt_ps.o
162		- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
163		+ $(CC) $(LDFLAGS) $(CPPFLAGS) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
164
165		lav2svg : lav2plt.o lavplt_svg.o
166		- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
167		+ $(CC) $(LDFLAGS) $(CPPFLAGS) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm

+229

-224

debian/patches/adjust-scripts less more

0	0	Author: Michael R. Crusoe <michael.crusoe@gmail.com>
1	1	Description: adjust for installed use
2		--- fasta3.orig/scripts/ann_exons_all.pl
3		+++ fasta3/scripts/ann_exons_all.pl
4		@@ -1,4 +1,4 @@
5		-#!/usr/bin/env perl
6		+#!/usr/bin/perl
7
8		################################################################
9		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
10		--- fasta3.orig/scripts/ann_exons_ens.pl
11		+++ fasta3/scripts/ann_exons_ens.pl
12		@@ -1,4 +1,4 @@
13		-#!/usr/bin/env perl
14		+#!/usr/bin/perl
15
16		################################################################
17		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
18		--- fasta3.orig/scripts/ann_exons_ncbi.pl
19		+++ fasta3/scripts/ann_exons_ncbi.pl
	2	--- a/scripts/ann_exons_all.pl
	3	+++ b/scripts/ann_exons_all.pl
	4	@@ -1,4 +1,4 @@
	5	-#!/usr/bin/env perl
	6	+#!/usr/bin/perl
	7
	8	################################################################
	9	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	10	--- a/scripts/ann_exons_ens.pl
	11	+++ b/scripts/ann_exons_ens.pl
	12	@@ -1,4 +1,4 @@
	13	-#!/usr/bin/env perl
	14	+#!/usr/bin/perl
	15
	16	################################################################
	17	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	18	--- a/scripts/ann_exons_ncbi.pl
	19	+++ b/scripts/ann_exons_ncbi.pl
20	20	@@ -1,4 +1,4 @@
21	21	-#!/usr/bin/env perl
22	22	+#!/usr/bin/perl
23	23
24	24	# ann_exons_ncbi.pl gets an annotation file from fasta36 -V with a line of the form:
25	25
26		--- fasta3.orig/scripts/ann_exons_up_sql.pl
27		+++ fasta3/scripts/ann_exons_up_sql.pl
28		@@ -1,4 +1,4 @@
29		-#!/usr/bin/env perl
30		+#!/usr/bin/perl
31
32		################################################################
33		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
34		--- fasta3.orig/scripts/ann_exons_up_sql_www.pl
35		+++ fasta3/scripts/ann_exons_up_sql_www.pl
36		@@ -1,4 +1,4 @@
37		-#!/usr/bin/env perl
38		+#!/usr/bin/perl
39
40		################################################################
41		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
42		--- fasta3.orig/scripts/ann_exons_up_www.pl
43		+++ fasta3/scripts/ann_exons_up_www.pl
44		@@ -1,4 +1,4 @@
45		-#!/usr/bin/env perl
46		+#!/usr/bin/perl
47
48		################################################################
49		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
50		--- fasta3.orig/scripts/ann_feats2ipr.pl
51		+++ fasta3/scripts/ann_feats2ipr.pl
	26	--- a/scripts/ann_exons_up_sql.pl
	27	+++ b/scripts/ann_exons_up_sql.pl
	28	@@ -1,4 +1,4 @@
	29	-#!/usr/bin/env perl
	30	+#!/usr/bin/perl
	31
	32	################################################################
	33	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	34	--- a/scripts/ann_exons_up_sql_www.pl
	35	+++ b/scripts/ann_exons_up_sql_www.pl
	36	@@ -1,4 +1,4 @@
	37	-#!/usr/bin/env perl
	38	+#!/usr/bin/perl
	39
	40	################################################################
	41	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	42	--- a/scripts/ann_exons_up_www.pl
	43	+++ b/scripts/ann_exons_up_www.pl
	44	@@ -1,4 +1,4 @@
	45	-#!/usr/bin/env perl
	46	+#!/usr/bin/perl
	47
	48	################################################################
	49	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	50	--- a/scripts/ann_feats2ipr.pl
	51	+++ b/scripts/ann_feats2ipr.pl
52	52	@@ -1,4 +1,4 @@
53	53	-#!/usr/bin/env perl
54	54	+#!/usr/bin/perl
55	55
56	56	################################################################
57	57	# copyright (c) 2014 by William R. Pearson and The Rector &
58		--- fasta3.orig/scripts/ann_feats2ipr_e.pl
59		+++ fasta3/scripts/ann_feats2ipr_e.pl
	58	--- a/scripts/ann_feats2ipr_e.pl
	59	+++ b/scripts/ann_feats2ipr_e.pl
60	60	@@ -1,4 +1,4 @@
61	61	-#!/usr/bin/env perl
62	62	+#!/usr/bin/perl
63	63
64	64	################################################################
65	65	# copyright (c) 2014 by William R. Pearson and The Rector &
66		--- fasta3.orig/scripts/ann_feats_up_sql.pl
67		+++ fasta3/scripts/ann_feats_up_sql.pl
68		@@ -1,4 +1,4 @@
69		-#!/usr/bin/env perl
70		+#!/usr/bin/perl
71
72		################################################################
73		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
74		--- fasta3.orig/scripts/ann_feats_up_www2.pl
75		+++ fasta3/scripts/ann_feats_up_www2.pl
76		@@ -1,4 +1,4 @@
77		-#!/usr/bin/env perl
78		+#!/usr/bin/perl
79
80		################################################################
81		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
82		--- fasta3.orig/scripts/ann_ipr_www.pl
83		+++ fasta3/scripts/ann_ipr_www.pl
	66	--- a/scripts/ann_feats_up_sql.pl
	67	+++ b/scripts/ann_feats_up_sql.pl
	68	@@ -1,4 +1,4 @@
	69	-#!/usr/bin/env perl
	70	+#!/usr/bin/perl
	71
	72	################################################################
	73	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	74	--- a/scripts/ann_feats_up_www2.pl
	75	+++ b/scripts/ann_feats_up_www2.pl
	76	@@ -1,4 +1,4 @@
	77	-#!/usr/bin/env perl
	78	+#!/usr/bin/perl
	79
	80	################################################################
	81	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	82	--- a/scripts/ann_ipr_www.pl
	83	+++ b/scripts/ann_ipr_www.pl
84	84	@@ -1,4 +1,4 @@
85	85	-#!/usr/bin/env perl
86	86	+#!/usr/bin/perl
87	87
88	88	################################################################
89	89	# copyright (c) 2014 by William R. Pearson and The Rector &
90		--- fasta3.orig/scripts/ann_pdb_cath.pl
91		+++ fasta3/scripts/ann_pdb_cath.pl
	90	--- a/scripts/ann_pdb_cath.pl
	91	+++ b/scripts/ann_pdb_cath.pl
92	92	@@ -1,4 +1,4 @@
93	93	-#!/usr/bin/env perl
94	94	+#!/usr/bin/perl
95	95
96	96	################################################################
97	97	# copyright (c) 2014 by William R. Pearson and The Rector &
98		--- fasta3.orig/scripts/ann_pdb_vast.pl
99		+++ fasta3/scripts/ann_pdb_vast.pl
	98	--- a/scripts/ann_pdb_vast.pl
	99	+++ b/scripts/ann_pdb_vast.pl
100	100	@@ -1,4 +1,4 @@
101	101	-#!/usr/bin/env perl
102	102	+#!/usr/bin/perl
103	103
104	104	################################################################
105	105	# copyright (c) 2014, 2015 by William R. Pearson and The Rector &
106		--- fasta3.orig/scripts/ann_pfam30_tmptbl.pl
107		+++ fasta3/scripts/ann_pfam30_tmptbl.pl
108		@@ -1,4 +1,4 @@
109		-#!/usr/bin/env perl
110		+#!/usr/bin/perl
111
112		################################################################
113		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
114		--- fasta3.orig/scripts/ann_pfam_sql.pl
115		+++ fasta3/scripts/ann_pfam_sql.pl
	106	--- a/scripts/ann_pfam30_tmptbl.pl
	107	+++ b/scripts/ann_pfam30_tmptbl.pl
	108	@@ -1,4 +1,4 @@
	109	-#!/usr/bin/env perl
	110	+#!/usr/bin/perl
	111
	112	################################################################
	113	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	114	--- a/scripts/ann_pfam_sql.pl
	115	+++ b/scripts/ann_pfam_sql.pl
116	116	@@ -1,4 +1,4 @@
117	117	-#!/usr/bin/env perl
118	118	+#!/usr/bin/perl
119	119
120	120	################################################################
121	121	# copyright (c) 2015 by William R. Pearson and The Rector &
122		--- fasta3.orig/scripts/ann_pfam_www.pl
123		+++ fasta3/scripts/ann_pfam_www.pl
	122	--- a/scripts/ann_pfam_www.pl
	123	+++ b/scripts/ann_pfam_www.pl
124	124	@@ -1,4 +1,4 @@
125	125	-#!/usr/bin/env perl
126	126	+#!/usr/bin/perl
127	127
128	128	################################################################
129	129	# copyright (c) 2014, 2015 by William R. Pearson and The Rector &
130		--- fasta3.orig/scripts/ann_upfeats_pfam_www_e.pl
131		+++ fasta3/scripts/ann_upfeats_pfam_www_e.pl
	130	--- a/scripts/ann_upfeats_pfam_www_e.pl
	131	+++ b/scripts/ann_upfeats_pfam_www_e.pl
132	132	@@ -1,4 +1,4 @@
133	133	-#!/usr/bin/env perl
134	134	+#!/usr/bin/perl
135	135
136	136	################################################################
137	137	# copyright (c) 2014 by William R. Pearson and The Rector &
138		--- fasta3.orig/scripts/annot_blast_btop2.pl
139		+++ fasta3/scripts/annot_blast_btop2.pl
	138	--- a/scripts/annot_blast_btop2.pl
	139	+++ b/scripts/annot_blast_btop2.pl
140	140	@@ -1,4 +1,4 @@
141	141	-#!/usr/bin/env perl
142	142	+#!/usr/bin/perl
143	143
144	144	################################################################
145	145	# copyright (c) 2017,2018 by William R. Pearson and The Rector &
146		--- fasta3.orig/scripts/annot_blast_btop3.py
147		+++ fasta3/scripts/annot_blast_btop3.py
	146	--- a/scripts/annot_blast_btop3.py
	147	+++ b/scripts/annot_blast_btop3.py
148	148	@@ -1,4 +1,4 @@
149	149	-#!/usr/bin/env python3
150	150	+#!/usr/bin/python3
151	151
152	152	################################################################
153	153	# copyright (c) 2017,2018 by William R. Pearson and The Rector &
154		--- fasta3.orig/scripts/annot_blast_btop4.py
155		+++ fasta3/scripts/annot_blast_btop4.py
	154	--- a/scripts/annot_blast_btop4.py
	155	+++ b/scripts/annot_blast_btop4.py
156	156	@@ -1,4 +1,4 @@
157	157	-#!/usr/bin/env python3
158	158	+#!/usr/bin/python3
159	159
160	160	################################################################
161	161	# copyright (c) 2017,2018 by William R. Pearson and The Rector &
162		--- fasta3.orig/scripts/blastp_annot_cmd.sh
163		+++ fasta3/scripts/blastp_annot_cmd.sh
164		@@ -55,14 +55,14 @@
	162	--- a/scripts/blastp_annot_cmd.sh
	163	+++ b/scripts/blastp_annot_cmd.sh
	164	@@ -82,19 +82,19 @@ $BLAST_PATH/blast_formatter -archive $bl
	165
	166	# annot_cmd="annot_blast_btop2.pl --query $QUERY --raw --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann"
	167	# echo "# $annot_cmd"
	168	-annot_blast_btop2.pl --query $QUERY --raw --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
	169	+/usr/share/fasta3/scripts/annot_blast_btop2.pl --query $QUERY --raw --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
	170
	171	if [[ $DO_HTML == 1 ]]; then
	172	## rename_exons.py --have_qslen --dom_info $blt_ann > $blr_out
	173	$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 -html > $bl0_out
	174	## echo "# merge_blast_btab.pl --plot_url=plot_domain6t.cgi --have_qslen --dom_info --btab $blt_out $bl0_out"
	175	- merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blt_ann $bl0_out
	176	+ /usr/share/fasta3/scripts/merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blt_ann $bl0_out
	177
	178	else
	179	$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 > $bl0_out
	180	merge_cmd="merge_blast_btab.pl --have_qslen --dom_info --btab $blt_ann $bl0_out"
	181	# echo "# $merge_cmd"
	182	- merge_blast_btab.pl --have_qslen --dom_info --btab $blt_ann $bl0_out
	183	+ /usr/share/fasta3/scripts/merge_blast_btab.pl --have_qslen --dom_info --btab $blt_ann $bl0_out
	184	fi
	185
	186	# $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 2 > $blm_out
	187	--- a/scripts/blastp_cmd.sh
	188	+++ b/scripts/blastp_cmd.sh
	189	@@ -22,7 +22,7 @@ blt_out="$OUTNAME.bl_tab"
165	190	# echo "OUTFILE = ${OUTNAME}"
166	191
167	192	#export BLAST_PATH="/ebi/extserv/bin/ncbi-blast+/bin"

170	195
171	196	$BLAST_PATH/blastp -outfmt 11 $cmd > $bl_asn
172	197	$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 -html > $bl0_out
173		$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
174		-annot_blast_btop2.pl --query $QUERY --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
175		+/usr/share/fasta3/scripts/annot_blast_btop2.pl --query $QUERY --have_qslen --dom_info --ann_script "$ANN_SCRIPT" --q_ann_script "$Q_ANN_SCRIPT" $blt_out > $blt_ann
176
177		## rename_exons.py --have_qslen --dom_info $blt_ann > $blr_out
178		-merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
179		+/usr/share/fasta3/scripts/merge_blast_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
180
181		# $BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 2 > $blm_out
182		--- fasta3.orig/scripts/blastp_cmd.sh
183		+++ fasta3/scripts/blastp_cmd.sh
184		@@ -22,7 +22,7 @@
185		# echo "OUTFILE = ${OUTNAME}"
186
187		#export BLAST_PATH="/ebi/extserv/bin/ncbi-blast+/bin"
188		-export BLAST_PATH="/seqprg/bin"
189		+export BLAST_PATH="/usr/bin"
190
191		$BLAST_PATH/blastp -outfmt 11 $cmd > $bl_asn
192		$BLAST_PATH/blast_formatter -archive $bl_asn -outfmt 0 -html > $bl0_out
193		--- fasta3.orig/scripts/exp_up_ensg.pl
194		+++ fasta3/scripts/exp_up_ensg.pl
	198	--- a/scripts/exp_up_ensg.pl
	199	+++ b/scripts/exp_up_ensg.pl
195	200	@@ -1,4 +1,4 @@
196	201	-#!/usr/bin/env perl
197	202	+#!/usr/bin/perl
198	203
199	204	################################################################
200	205	# copyright (c) 2010, 2014 by William R. Pearson and The Rector &
201		--- fasta3.orig/scripts/expand_links.pl
202		+++ fasta3/scripts/expand_links.pl
	206	--- a/scripts/expand_links.pl
	207	+++ b/scripts/expand_links.pl
203	208	@@ -1,4 +1,4 @@
204	209	-#!/usr/bin/env perl
205	210	+#!/usr/bin/perl
206	211
207	212	################################################################
208	213	# copyright (c) 2010, 2014 by William R. Pearson and The Rector &
209		--- fasta3.orig/scripts/expand_refseq_isoforms.pl
210		+++ fasta3/scripts/expand_refseq_isoforms.pl
	214	--- a/scripts/expand_refseq_isoforms.pl
	215	+++ b/scripts/expand_refseq_isoforms.pl
211	216	@@ -1,4 +1,4 @@
212	217	-#!/usr/bin/env perl
213	218	+#!/usr/bin/perl
214	219
215	220	################################################################
216	221	# copyright (c) 2010, 2014 by William R. Pearson and The Rector &
217		--- fasta3.orig/scripts/expand_uniref50.pl
218		+++ fasta3/scripts/expand_uniref50.pl
	222	--- a/scripts/expand_uniref50.pl
	223	+++ b/scripts/expand_uniref50.pl
219	224	@@ -1,4 +1,4 @@
220	225	-#!/usr/bin/env perl
221	226	+#!/usr/bin/perl
222	227
223	228	################################################################
224	229	# copyright (c) 2010, 2014 by William R. Pearson and The Rector &
225		--- fasta3.orig/scripts/expand_up_isoforms.pl
226		+++ fasta3/scripts/expand_up_isoforms.pl
	230	--- a/scripts/expand_up_isoforms.pl
	231	+++ b/scripts/expand_up_isoforms.pl
227	232	@@ -1,4 +1,4 @@
228	233	-#!/usr/bin/env perl
229	234	+#!/usr/bin/perl
230	235
231	236	################################################################
232	237	# copyright (c) 2010, 2014 by William R. Pearson and The Rector &
233		--- fasta3.orig/scripts/fasta_annot_cmd.sh
234		+++ fasta3/scripts/fasta_annot_cmd.sh
235		@@ -54,7 +54,7 @@
	238	--- a/scripts/fasta_annot_cmd.sh
	239	+++ b/scripts/fasta_annot_cmd.sh
	240	@@ -54,7 +54,7 @@ bla_out="${OUTNAME}_an.html"
236	241	blt_out="$OUTNAME.fa_tab"
237	242	blr_out="$OUTNAME.fa_tab_rn"
238	243

241	246	# BLAST_PATH="../bin"
242	247
243	248	cmd="$cmd -mF8CBL=$blt_out $QUERY $DATABASE"
244		@@ -73,7 +73,7 @@
	249	@@ -73,7 +73,7 @@ cmd="$cmd -mF8CBL=$blt_out $QUERY $DATAB
245	250	# run the program
246	251	$BLAST_PATH/$SRCH_CMD $cmd > $bl0_out
247	252

250	255
251	256	if [ ! -s $blr_out ]; then
252	257	# echo "# " `ls -l $blt_out $blr_out`
253		@@ -81,4 +81,4 @@
	258	@@ -81,4 +81,4 @@ if [ ! -s $blr_out ]; then
254	259	# echo "# " `ls -l $blt_out $blr_out`
255	260	fi
256	261
257	262	-$BLAST_PATH/merge_fasta_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
258	263	+/usr/share/fasta3/scripts/merge_fasta_btab.pl --plot_url="plot_domain6t.cgi" --have_qslen --dom_info --btab $blr_out $bl0_out
259		--- fasta3.orig/scripts/get_genome_seq.py
260		+++ fasta3/scripts/get_genome_seq.py
	264	--- a/scripts/get_genome_seq.py
	265	+++ b/scripts/get_genome_seq.py
261	266	@@ -1,4 +1,4 @@
262	267	-#!/usr/bin/env python3
263	268	+#!/usr/bin/python3
264	269
265	270	################
266	271	## get_hg38_bed.py parses an HG38 coordinate into a pseudo-bed entry,
267		--- fasta3.orig/scripts/get_protein.py
268		+++ fasta3/scripts/get_protein.py
	272	--- a/scripts/get_protein.py
	273	+++ b/scripts/get_protein.py
269	274	@@ -1,4 +1,4 @@
270	275	-#!/usr/bin/env python3
271	276	+#!/usr/bin/python3
272	277
273	278	## get_protein_www.py --
274	279	## get a protein sequence from the Uniprot or NCBI/Refseq web sites using the accession
275		--- fasta3.orig/scripts/get_protein_sql.py
276		+++ fasta3/scripts/get_protein_sql.py
	280	--- a/scripts/get_protein_sql.py
	281	+++ b/scripts/get_protein_sql.py
277	282	@@ -1,4 +1,4 @@
278	283	-#!/usr/bin/env python
279	284	+#!/usr/bin/python3
280	285
281	286	## get_protein_sql.py --
282	287	## get a protein sequence from a local Uniprot or NCBI/Refseq mySQL database using the accession
283		--- fasta3.orig/scripts/get_protein_sql_www.py
284		+++ fasta3/scripts/get_protein_sql_www.py
	288	--- a/scripts/get_protein_sql_www.py
	289	+++ b/scripts/get_protein_sql_www.py
285	290	@@ -1,4 +1,4 @@
286	291	-#!/usr/bin/env python3
287	292	+#!/usr/bin/python3
288	293
289	294	## get_protein.py --
290	295	## get a protein sequence from Uniprot or NCBI/Refseq using the accession
291		--- fasta3.orig/scripts/get_refseq.py
292		+++ fasta3/scripts/get_refseq.py
	296	--- a/scripts/get_refseq.py
	297	+++ b/scripts/get_refseq.py
293	298	@@ -1,4 +1,4 @@
294	299	-#!/usr/bin/env python3
295	300	+#!/usr/bin/python3
296	301
297	302	import sys
298	303	import re
299		--- fasta3.orig/scripts/get_uniprot.py
300		+++ fasta3/scripts/get_uniprot.py
	304	--- a/scripts/get_uniprot.py
	305	+++ b/scripts/get_uniprot.py
301	306	@@ -1,4 +1,4 @@
302	307	-#!/usr/bin/env python3
303	308	+#!/usr/bin/python3
304	309
305	310	import sys
306	311	import re
307		--- fasta3.orig/scripts/get_up_prot_iso_sql.py
308		+++ fasta3/scripts/get_up_prot_iso_sql.py
	312	--- a/scripts/get_up_prot_iso_sql.py
	313	+++ b/scripts/get_up_prot_iso_sql.py
309	314	@@ -1,4 +1,4 @@
310	315	-#!/usr/bin/env python3
311	316	+#!/usr/bin/python3
312	317
313	318	import sys
314	319	import re
315		--- fasta3.orig/scripts/lav2plt.pl
316		+++ fasta3/scripts/lav2plt.pl
	320	--- a/scripts/lav2plt.pl
	321	+++ b/scripts/lav2plt.pl
317	322	@@ -1,4 +1,4 @@
318	323	-#!/usr/bin/env perl
319	324	+#!/usr/bin/perl
320	325
321	326	# lav2plt.pl - produce plotfrom lav output */
322	327
323		--- fasta3.orig/scripts/lavplt_ps.pl
324		+++ fasta3/scripts/lavplt_ps.pl
	328	--- a/scripts/lavplt_ps.pl
	329	+++ b/scripts/lavplt_ps.pl
325	330	@@ -1,4 +1,4 @@
326	331	-#!/usr/bin/env perl
327	332	+#!/usr/bin/perl
328	333	#
329	334	################################################################
330	335	# copyright (c) 2012, 2014 by William R. Pearson and The Rector &
331		--- fasta3.orig/scripts/lavplt_svg.pl
332		+++ fasta3/scripts/lavplt_svg.pl
	336	--- a/scripts/lavplt_svg.pl
	337	+++ b/scripts/lavplt_svg.pl
333	338	@@ -1,4 +1,4 @@
334	339	-#!/usr/bin/env perl
335	340	+#!/usr/bin/perl
336	341	#
337	342	################################################################
338	343	# copyright (c) 2012, 2014 by William R. Pearson and The Rector &
339		--- fasta3.orig/scripts/links2sql.pl
340		+++ fasta3/scripts/links2sql.pl
	344	--- a/scripts/links2sql.pl
	345	+++ b/scripts/links2sql.pl
341	346	@@ -1,4 +1,4 @@
342	347	-#!/usr/bin/env perl
343	348	+#!/usr/bin/perl
344	349
345	350	################################################################
346	351	# copyright (c) 2014 by William R. Pearson and The Rector &
347		--- fasta3.orig/scripts/m8_btop_msa.pl
348		+++ fasta3/scripts/m8_btop_msa.pl
349		@@ -1,4 +1,4 @@
350		-#!/usr/bin/env perl
351		+#!/usr/bin/perl
352
353		################################################################
354		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
355		--- fasta3.orig/scripts/m9B_btop_msa.pl
356		+++ fasta3/scripts/m9B_btop_msa.pl
357		@@ -1,4 +1,4 @@
358		-#!/usr/bin/env perl
359		+#!/usr/bin/perl
360
361		################################################################
362		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
363		--- fasta3.orig/scripts/map_exon_coords.py
364		+++ fasta3/scripts/map_exon_coords.py
	352	--- a/scripts/m8_btop_msa.pl
	353	+++ b/scripts/m8_btop_msa.pl
	354	@@ -1,4 +1,4 @@
	355	-#!/usr/bin/env perl
	356	+#!/usr/bin/perl
	357
	358	################################################################
	359	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	360	--- a/scripts/m9B_btop_msa.pl
	361	+++ b/scripts/m9B_btop_msa.pl
	362	@@ -1,4 +1,4 @@
	363	-#!/usr/bin/env perl
	364	+#!/usr/bin/perl
	365
	366	################################################################
	367	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	368	--- a/scripts/map_exon_coords.py
	369	+++ b/scripts/map_exon_coords.py
365	370	@@ -1,4 +1,4 @@
366	371	-#!/usr/bin/env python3
367	372	+#!/usr/bin/python3
368	373	#
369	374	# given a -m8CB file with exon annotations for the query and subject,
370	375	# provide a function that maps subject coordinates to query, or vice versa
371		--- fasta3.orig/scripts/merge_blast_btab.pl
372		+++ fasta3/scripts/merge_blast_btab.pl
	376	--- a/scripts/merge_blast_btab.pl
	377	+++ b/scripts/merge_blast_btab.pl
373	378	@@ -1,4 +1,4 @@
374	379	-#!/usr/bin/env perl
375	380	+#!/usr/bin/perl
376	381
377	382	################################################################
378	383	# copyright (c) 2018 by William R. Pearson and The Rector &
379		--- fasta3.orig/scripts/merge_fasta_btab.pl
380		+++ fasta3/scripts/merge_fasta_btab.pl
	384	--- a/scripts/merge_fasta_btab.pl
	385	+++ b/scripts/merge_fasta_btab.pl
381	386	@@ -1,4 +1,4 @@
382	387	-#!/usr/bin/env perl
383	388	+#!/usr/bin/perl
384	389
385	390	################################################################
386	391	# copyright (c) 2018 by William R. Pearson and The Rector &
387		--- fasta3.orig/scripts/relabel_domains.py
388		+++ fasta3/scripts/relabel_domains.py
389		@@ -1,4 +1,4 @@
390		-#!/usr/bin/env python3
391		+#!/usr/bin/python3
392
393		# Given a blast_tabular file with search results from one or more protein queries
394		#
395		--- fasta3.orig/scripts/rename_exons.py
396		+++ fasta3/scripts/rename_exons.py
	392	--- a/scripts/relabel_domains.py
	393	+++ b/scripts/relabel_domains.py
	394	@@ -1,4 +1,4 @@
	395	-#!/usr/bin/env python3
	396	+#!/usr/bin/python3
	397
	398	# Given a blast_tabular file with search results from one or more
	399	# protein queries, modify the domain color numbers (e.g. ~1, ~2) so
	400	--- a/scripts/rename_exons.py
	401	+++ b/scripts/rename_exons.py
397	402	@@ -1,4 +1,4 @@
398	403	-#!/usr/bin/env python3
399	404	+#!/usr/bin/python3
400	405	#
401	406	# given a -m8CB file with exon annotations for the query and subject,
402	407	# adjust the subject exon names to match the query exon names
403		--- fasta3.orig/scripts/summ_domain_ident.pl
404		+++ fasta3/scripts/summ_domain_ident.pl
	408	--- a/scripts/summ_domain_ident.pl
	409	+++ b/scripts/summ_domain_ident.pl
405	410	@@ -1,4 +1,4 @@
406	411	-#!/usr/bin/env perl
407	412	+#!/usr/bin/perl
408	413
409	414	################################################################
410	415	# copyright (c) 2014 by William R. Pearson and The Rector &
411		--- fasta3.orig/scripts/test_py.sh
412		+++ fasta3/scripts/test_py.sh
	416	--- a/scripts/test_py.sh
	417	+++ b/scripts/test_py.sh
413	418	@@ -5,57 +5,58 @@
414	419	## test python scripts
415	420	##

502	507	+# echo '.bl_tab yes raw score'
503	508	+# /usr/share/fasta3/scripts/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
504	509
505		--- fasta3.orig/scripts/test_ann_scripts.sh
506		+++ fasta3/scripts/test_ann_scripts.sh
	510	--- a/scripts/test_ann_scripts.sh
	511	+++ b/scripts/test_ann_scripts.sh
507	512	@@ -9,22 +9,22 @@
508	513	# SP:GSTM1_HUMAN -- ebi searches without accession
509	514	##

538	543	+ done < ${ex_file}
539	544	+ echo '*DONE*' "$script" "$(date)"
540	545	+done < ${script_file}
541		--- fasta3.orig/scripts/ann_script_list
542		+++ fasta3/scripts/ann_script_list
	546	--- a/scripts/ann_script_list
	547	+++ b/scripts/ann_script_list
543	548	@@ -1,9 +1,7 @@
544	549	-ann_exons_up_sql.pl
545	550	-ann_exons_up_www.pl

557	562	+/usr/share/fasta3/scripts/ann_feats_up_www2.pl
558	563	+/usr/share/fasta3/scripts/ann_ipr_www.pl
559	564	+/usr/share/fasta3/scripts/ann_upfeats_pfam_www_e.pl
560		--- fasta3.orig/psisearch2/clustal2fasta.pl
561		+++ fasta3/psisearch2/clustal2fasta.pl
562		@@ -1,4 +1,4 @@
563		-#!/usr/bin/env perl
564		+#!/usr/bin/perl
565
566		################################################################
567		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
568		--- fasta3.orig/psisearch2/clustal2fasta.py
569		+++ fasta3/psisearch2/clustal2fasta.py
	565	--- a/psisearch2/clustal2fasta.pl
	566	+++ b/psisearch2/clustal2fasta.pl
	567	@@ -1,4 +1,4 @@
	568	-#!/usr/bin/env perl
	569	+#!/usr/bin/perl
	570
	571	################################################################
	572	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	573	--- a/psisearch2/clustal2fasta.py
	574	+++ b/psisearch2/clustal2fasta.py
570	575	@@ -1,4 +1,4 @@
571	576	-#!/usr/bin/env python
572	577	+#!/usr/bin/python3
573	578
574	579	################################################################
575	580	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
576		--- fasta3.orig/psisearch2/m89_btop_msa2.pl
577		+++ fasta3/psisearch2/m89_btop_msa2.pl
578		@@ -1,4 +1,4 @@
579		-#!/usr/bin/env perl
580		+#!/usr/bin/perl
581
582		################################################################
583		# copyright (c) 2014,2015 by William R. Pearson and The Rector &
584		--- fasta3.orig/psisearch2/psisearch2_msa.pl
585		+++ fasta3/psisearch2/psisearch2_msa.pl
586		@@ -1,4 +1,4 @@
587		-#!/usr/bin/env perl
588		+#!/usr/bin/perl
589
590		################################################################
591		# copyright (c) 2016 by William R. Pearson and The Rector &
592		@@ -48,7 +48,7 @@
	581	--- a/psisearch2/m89_btop_msa2.pl
	582	+++ b/psisearch2/m89_btop_msa2.pl
	583	@@ -1,4 +1,4 @@
	584	-#!/usr/bin/env perl
	585	+#!/usr/bin/perl
	586
	587	################################################################
	588	# copyright (c) 2014,2015 by William R. Pearson and The Rector &
	589	--- a/psisearch2/psisearch2_msa.pl
	590	+++ b/psisearch2/psisearch2_msa.pl
	591	@@ -1,4 +1,4 @@
	592	-#!/usr/bin/env perl
	593	+#!/usr/bin/perl
	594
	595	################################################################
	596	# copyright (c) 2016,2020 by William R. Pearson and The Rector &
	597	@@ -54,7 +54,7 @@ use vars qw( $prev_m89res $m_format $pre
593	598	# (3) NCBI blast+ programs: psiblast/makeblastdb
594	599	# (4) NCBI datatool (required only for ssearch36 PSSMs)
595	600
596	601	-my $pgm_bin = "/seqprg/bin";
597	602	+my $pgm_bin = "/usr/bin";
	603
598	604	my $pgm_data = "/seqprg/data";
599	605	my $ssearch_bin = "$pgm_bin/ssearch36";
600		my $psiblast_bin = "$pgm_bin/psiblast";
601		--- fasta3.orig/psisearch2/psisearch2_msa.py
602		+++ fasta3/psisearch2/psisearch2_msa.py
	606	--- a/psisearch2/psisearch2_msa.py
	607	+++ b/psisearch2/psisearch2_msa.py
603	608	@@ -1,4 +1,4 @@
604	609	-#!/usr/bin/env python
605	610	+#!/usr/bin/python3
606	611
607	612	################################################################
608	613	# copyright (c) 2016 by William R. Pearson and The Rector &
609		@@ -45,7 +45,7 @@
	614	@@ -45,7 +45,7 @@ import re
610	615	# (3) NCBI blast+ programs: psiblast/makeblastdb
611	616	# (4) NCBI datatool (required only for ssearch36 PSSMs)
612	617

615	620	pgm_data = "/seqprg/data"
616	621	ssearch_bin = pgm_bin+"/ssearch36"
617	622	psiblast_bin = pgm_bin+"/psiblast"
618		@@ -54,9 +54,9 @@
	623	@@ -54,9 +54,9 @@ datatool_bin = "%s/datatool -m %s/NCBI_a
619	624	align2msa_lib = "m89_btop_msa2.pl"
620	625	clustal2fasta = "clustal2fasta.py"
621	626

628	633
629	634	num_iter = 5
630	635	srch_pgm = 'ssearch'
631		--- fasta3.orig/psisearch2/psisearch2_msa_iter.sh
632		+++ fasta3/psisearch2/psisearch2_msa_iter.sh
	636	--- a/psisearch2/psisearch2_msa_iter.sh
	637	+++ b/psisearch2/psisearch2_msa_iter.sh
633	638	@@ -7,8 +7,8 @@
634	639	#
635	640

641	646	FA_DB=/slib2/fa_dbs/qfo78.lseg
642	647	BL_DB=/slib2/bl_dbs/qfo78
643	648	DB=$FA_DB
644		--- fasta3.orig/psisearch2/psisearch2_msa_iter_bl.sh
645		+++ fasta3/psisearch2/psisearch2_msa_iter_bl.sh
	649	--- a/psisearch2/psisearch2_msa_iter_bl.sh
	650	+++ b/psisearch2/psisearch2_msa_iter_bl.sh
646	651	@@ -6,7 +6,7 @@
647	652	# psisearch2_msa.pl --pgm psiblast --query query.aa --num_iter 5 --db /slib2/bl_dbs/qfo78
648	653	#

-65

debian/patches/local_tests less more

0	0	Author: Michael R. Crusoe <michael.crusoe@gmail.com>
1	1	Description: disable tests that require external databases
2		--- fasta3.orig/test/test.sh
3		+++ fasta3/test/test.sh
4		@@ -7,71 +7,71 @@
	2	--- a/test/test.sh
	3	+++ b/test/test.sh
	4	@@ -7,71 +7,13 @@ if [ ! -d results ]; then
5	5	mkdir results
6	6	fi
7	7
8		-export FA_DB=/slib2/fa_dbs/qfo20.lseg
	8	-export FA_DB=$SLIB2/fa_dbs/qfo20.lseg
9	9	-
10	10	-echo "starting fasta36 - protein" `date`
11	11	-../bin/fasta36 -q -m 6 -Z 100000 ../seq/mgstm1.aa:1-100 $FA_DB > results/test_m1.ok2.html

32	32	- ../bin/ssearch36s -q -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa $FA_DB > results/test_m1.sss_p25
33	33	- echo "done"
34	34	-fi
35		+# export FA_DB=/slib2/fa_dbs/qfo20.lseg
36		+#
37		+# echo "starting fasta36 - protein" `date`
38		+# ../bin/fasta36 -q -m 6 -Z 100000 ../seq/mgstm1.aa:1-100 $FA_DB > results/test_m1.ok2.html
39		+# ../bin/fasta36 -S -q -z 11 -O results/test_m1.ok2_p25 -s P250 ../seq/mgstm1.aa:100-218 $FA_DB
40		+# echo "done"
41		+# echo "starting fastxy36" `date`
42		+# ../bin/fastx36 -m 9c -S -q ../seq/mgtt2_x.seq $FA_DB 1 > results/test_t2.xk1
43		+# ../bin/fasty36 -S -q ../seq/mgtt2_x.seq $FA_DB > results/test_t2.yk2
44		+# ../bin/fastx36 -m 9c -S -q -z 2 ../seq/mgstm1.esq $FA_DB > results/test_m1.xk2z2
45		+# ../bin/fasty36 -S -q -z 2 ../seq/mgstm1.esq $FA_DB > results/test_m1.yk2z2
46		+# echo "done"
47		+# echo "starting fastxy36 rev" `date`
48		+# ../bin/fastx36 -m 9c -q -m 5 ../seq/mgstm1.rev $FA_DB > results/test_m1.xk2r
49		+# ../bin/fasty36 -q -m 5 -M 200-300 -z 2 ../seq/mgstm1.rev $FA_DB > results/test_m1.yk2rz2
50		+# ../bin/fasty36 -q -m 5 -z 11 ../seq/mgstm1.rev $FA_DB > results/test_m1.yk2rz11
51		+# echo "done"
52		+# echo "starting ssearch36" `date`
53		+# ../bin/ssearch36 -m 9c -S -z 3 -q ../seq/mgstm1.aa $FA_DB > results/test_m1.ssz3
54		+# ../bin/ssearch36 -q -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa $FA_DB > results/test_m1.ss_p25
55		+# echo "done"
56		+# if [ -e ../bin/ssearch36s ]; then
57		+# echo "starting ssearch36s" `date`
58		+# ../bin/ssearch36s -m 9c -S -z 3 -q ../seq/mgstm1.aa $FA_DB > results/test_m1.sssz3
59		+# ../bin/ssearch36s -q -M 200-300 -z 2 -Z 100000 -s P250 ../seq/mgstm1.aa $FA_DB > results/test_m1.sss_p25
60		+# echo "done"
61		+# fi
62	35	echo "starting prss36(ssearch/fastx)" `date`
63	36	../bin/ssearch36 -q -k 1000 -a ../seq/mgstm1.aa ../seq/xurt8c.aa > results/test_m1.rss
64	37	../bin/fastx36 -q -k 1000 ../seq/mgstm1.esq ../seq/xurt8c.aa > results/test_m1.rfx

73	46	-../bin/fasta36 -S -q ../seq/mgstm1.nt %RMB 4 > results/test_m1.ok4
74	47	-../bin/fasta36 -S -q ../seq/mgstm1.rev %RMB 4 > results/test_m1.ok4r
75	48	-echo "done"
76		+# echo "starting ggsearch36/glsearch36" `date`
77		+# ../bin/ggsearch36 -q -m 9i -w 80 ../seq/hahu.aa $FA_DB > results/test_h1.gg
78		+# ../bin/glsearch36 -q -m 9i -w 80 ../seq/hahu.aa $FA_DB > results/test_h1.gl
79		+# ../bin/ggsearch36 -q ../seq/gtt1_drome.aa $FA_DB > results/test_t1.gg
80		+# ../bin/glsearch36 -q ../seq/gtt1_drome.aa $FA_DB > results/test_t1.gl
81		+# echo "done"
82		+# echo "starting fasta36 - DNA" `date`
83		+# ../bin/fasta36 -S -q ../seq/mgstm1.nt %RMB 4 > results/test_m1.ok4
84		+# ../bin/fasta36 -S -q ../seq/mgstm1.rev %RMB 4 > results/test_m1.ok4r
85		+# echo "done"
86	49	#echo "starting tfasta36" `date`
87	50	#tfasta36 -q ../seq/mgstm1.aa %RMB > results/test_m1.tk2
88	51	#echo "done"

107	70	-echo "done"
108	71	-echo "starting tfasts36" `date`
109	72	-../bin/tfasts36 -q ../seq/n0.aa %r > results/test_m1.ts_r
110		+# echo "starting tfastxy36" `date`
111		+# ../bin/tfastx36 -m 9c -q -i -3 -m 6 ../seq/mgstm1.aa %p > results/test_m1.tx2.html
112		+# ../bin/tfasty36 -q -i -3 -N 5000 ../seq/mgstm1.aa %p > results/test_m1.ty2
113		+# echo "done"
114		+# echo "starting fastf36" `date`
115		+# ../bin/fastf36 -q ../seq/m1r.aa $FA_DB > results/test_mf.ff
116		+# ../bin/fastf36 -q ../seq/m1r.aa $FA_DB > results/test_mf.ff_s
117		+# echo "done"
118		+# echo "starting tfastf36" `date`
119		+# ../bin/tfastf36 -q ../seq/m1r.aa %r > results/test_mf.tfr
120		+# echo "done"
121		+# echo "starting fasts36" `date`
122		+# ../bin/fasts36 -q -V '*?@' ../seq/ngts.aa $FA_DB > results/test_m1.fs1
123		+# ../bin/fasts36 -q ../seq/ngt.aa $FA_DB > results/test_m1.fs
124		+# ../bin/fasts36 -q -n ../seq/mgstm1.nts m > results/test_m1.nfs
125		+# echo "starting fastm36" `date`
126		+# ../bin/fastm36 -q ../seq/ngts.aa $FA_DB > results/test_m1.fm
127		+# ../bin/fastm36 -q -n ../seq/mgstm1.nts m > results/test_m1.nfm
128		+# echo "done"
129		+# echo "starting tfasts36" `date`
130		+# ../bin/tfasts36 -q ../seq/n0.aa %r > results/test_m1.ts_r
131	73	echo "starting lalign36" `date`
132	74	../bin/lalign36 -k 1000 -q ../seq/mchu.aa ../seq/mchu.aa > results/test_mc.lal
133	75	../bin/lalign36 -z 3 -q ../seq/mchu.aa ../seq/mchu.aa > results/test_mc.lal_z3
134		--- fasta3.orig/test/test2G.sh
135		+++ fasta3/test/test2G.sh
136		@@ -6,69 +6,69 @@
	76	--- a/test/test2G.sh
	77	+++ b/test/test2G.sh
	78	@@ -6,69 +6,69 @@ echo ""
137	79	if [ ! -d results ]; then
138	80	mkdir results
139	81	fi

-1

debian/patches/series less more

0	0	Makefile.patch
1		simde
2	1	local_tests
3	2	adjust-scripts

-46

~~debian/patches/simde~~ less more

0		Author: Michael R. Crusoe <michael.crusoe@gmail.com>
1		Description: Fix compiling on non x86 with SIMD Everywhere
2		Forwarded: https://github.com/wrpearson/fasta36/pull/25
3
4		diff --git a/src/global_sse2.c b/src/global_sse2.c
5		index a5b2a3f..584bd67 100644
6		--- a/src/global_sse2.c
7		+++ b/src/global_sse2.c
8		@@ -19,7 +19,8 @@
9		#ifdef __SUNPRO_C
10		#include <sunmedia_intrin.h>
11		#else
12		-#include <emmintrin.h>
13		+#define SIMDE_ENABLE_NATIVE_ALIASES
14		+#include "simde/x86/sse2.h"
15		#endif
16
17		#ifdef SW_SSE2
18		diff --git a/src/glocal_sse2.c b/src/glocal_sse2.c
19		index d2e8348..123d270 100644
20		--- a/src/glocal_sse2.c
21		+++ b/src/glocal_sse2.c
22		@@ -19,7 +19,8 @@
23		#ifdef __SUNPRO_C
24		#include <sunmedia_intrin.h>
25		#else
26		-#include <emmintrin.h>
27		+#define SIMDE_ENABLE_NATIVE_ALIASES
28		+#include "simde/x86/sse2.h"
29		#endif
30
31		#ifdef SW_SSE2
32		diff --git a/src/smith_waterman_sse2.c b/src/smith_waterman_sse2.c
33		index d37f223..c638027 100644
34		--- a/src/smith_waterman_sse2.c
35		+++ b/src/smith_waterman_sse2.c
36		@@ -20,7 +20,8 @@
37		#ifdef __SUNPRO_C
38		#include <sunmedia_intrin.h>
39		#else
40		-#include <emmintrin.h>
41		+#define SIMDE_ENABLE_NATIVE_ALIASES
42		+#include "simde/x86/sse2.h"
43		#endif
44
45		#ifdef SW_SSE2