obitools/sumaclust
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 4 Wiki Activity

Compare commits

base: obitools:sumaclust_v1.0.32
Branches Tags
obitools:master
obitools:sumaclust_v1.0.34 obitools:sumaclust_v1.0.33 obitools:sumaclust_v1.0.32 obitools:sumaclust_v1.0.31 obitools:sumaclust_v1.0.20 obitools:sumaclust_v1.0.10
...
compare: obitools:master
Branches Tags
obitools:master
obitools:sumaclust_v1.0.34 obitools:sumaclust_v1.0.33 obitools:sumaclust_v1.0.32 obitools:sumaclust_v1.0.31 obitools:sumaclust_v1.0.20 obitools:sumaclust_v1.0.10

6 Commits
sumaclust_ ... master

Author SHA1 Message Date
coissac
777dfde26f Actualiser .gitmodules 2025-06-12 15:13:12 +00:00
Celine Mercier
8ca0c731ac moved sumalib to v1.0.36 2020-04-13 14:04:18 +02:00
Celine Mercier
361ecb23f5 version 1.0.35: edited sumalibs includes to work with some compilers 2020-04-01 15:15:15 +02:00
Celine Mercier
b85cdcfac1 forgotten pdf doc 2019-03-28 14:54:55 +01:00
Celine Mercier
2f0e2705ec updated documentation for the new installation 2019-03-28 14:45:48 +01:00
Celine Mercier
2e432e8381 Cleaner installation 2019-03-27 17:09:01 +01:00
7 changed files with 25 additions and 16 deletions
Expand all files Collapse all files

2
.gitmodules vendored
View File

@ -1,3 +1,3 @@
[submodule "sumalibs"] [submodule "sumalibs"]
path = sumalibs path = sumalibs
url = https://git.metabarcoding.org/obitools/sumalibs.git url = https://forge.metabarcoding.org/obitools/sumalibs.git

8
Makefile
View File

@ -1,3 +1,7 @@
PREFIX=/usr/local
CFLAGS=-I$(PREFIX)/include
EXEC = sumaclust EXEC = sumaclust
SUMACLUST_SRC = sumaclust.c \ SUMACLUST_SRC = sumaclust.c \
@ -42,3 +46,7 @@ clean:
rm -f $(EXEC) rm -f $(EXEC)
$(MAKE) -C ./sumalibs clean $(MAKE) -C ./sumalibs clean
install: all
install -d $(DESTDIR)$(PREFIX)/bin/
install -m 755 $(EXEC) $(DESTDIR)$(PREFIX)/bin/

8
mtcompare_sumaclust.c
View File

@ -15,10 +15,10 @@
#include <math.h> #include <math.h>
#include <sys/time.h> #include <sys/time.h>
#include "./sumalibs/libfasta/sequence.h" #include "sumalibs/libfasta/sequence.h"
#include "./sumalibs/libutils/utilities.h" #include "sumalibs/libutils/utilities.h"
#include "./sumalibs/liblcs/upperband.h" #include "sumalibs/liblcs/upperband.h"
#include "./sumalibs/liblcs/sse_banded_LCS_alignment.h" #include "sumalibs/liblcs/sse_banded_LCS_alignment.h"
#include "sumaclust.h" #include "sumaclust.h"

16
sumaclust.c
View File

@ -12,18 +12,18 @@
#include <math.h> #include <math.h>
#include <sys/time.h> #include <sys/time.h>
#include "./sumalibs/libutils/utilities.h" #include "sumalibs/libutils/utilities.h"
#include "./sumalibs/libfasta/sequence.h" #include "sumalibs/libfasta/sequence.h"
#include "./sumalibs/libfasta/fasta_header_parser.h" #include "sumalibs/libfasta/fasta_header_parser.h"
#include "./sumalibs/libfasta/fasta_header_handler.h" #include "sumalibs/libfasta/fasta_header_handler.h"
#include "./sumalibs/libfasta/fasta_seq_writer.h" #include "sumalibs/libfasta/fasta_seq_writer.h"
#include "./sumalibs/liblcs/upperband.h" #include "sumalibs/liblcs/upperband.h"
#include "./sumalibs/liblcs/sse_banded_LCS_alignment.h" #include "sumalibs/liblcs/sse_banded_LCS_alignment.h"
#include "mtcompare_sumaclust.h" #include "mtcompare_sumaclust.h"
#include "sumaclust.h" #include "sumaclust.h"
#define VERSION "1.0.32" #define VERSION "1.0.36"
/* ----------------------------------------------- */ /* ----------------------------------------------- */

3
sumaclust_user_manual.md
View File

@ -29,7 +29,8 @@ Untar the archive, go into the newly created directory and compile:
``` ```
tar –zxvf sumaclust_v[x.x.xx].tar.gz tar –zxvf sumaclust_v[x.x.xx].tar.gz
cd sumaclust_v[x.x.xx] cd sumaclust_v[x.x.xx]
make make -C sumalibs install
make install
``` ```
You can compile Sumaclust with `clang`, which deactivates `OpenMP`, with: You can compile Sumaclust with `clang`, which deactivates `OpenMP`, with:

BIN
sumaclust_user_manual.pdf
View File

Binary file not shown.

2
sumalibs

Submodule sumalibs updated: ed56cb1d6b...9f08b85eaf