Skip to content

Commit 1896610

Browse files
author
Hervé Rouault
committed
initial commit
0 parents  commit 1896610

32 files changed

+8039
-0
lines changed

‎.gitignore

+39
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,39 @@
1+
*~
2+
Makefile.in
3+
config.h.in
4+
config.h.in~
5+
configure
6+
depcomp
7+
build
8+
autoscan.log
9+
depcomp
10+
install-sh
11+
INSTALL
12+
missing
13+
py-compile
14+
aclocal.m4
15+
autom4te.cache
16+
depcomp
17+
compile
18+
mdate-sh
19+
texinfo.tex
20+
*.info
21+
stamp-vti
22+
version.texi
23+
tags
24+
*_cmdline.*
25+
cmdline.c
26+
cmdline.h
27+
.DS_Store
28+
test
29+
*.swp
30+
.version
31+
.tarball-version
32+
ltmain.sh
33+
m4/ltoptions.m4
34+
m4/ltsugar.m4
35+
m4/ltversion.m4
36+
m4/lt\~obsolete.m4
37+
m4/libtool.m4
38+
config.guess
39+
config.sub

‎AUTHORS

+4
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
1+
AUTHORS AND MAINTAINERS :
2+
3+
MAIN DEVELOPERS:
4+
Hervé Rouault <[email protected]>

‎COPYING

+674
Large diffs are not rendered by default.

‎ChangeLog

+4
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
1+
2011-08-04 Hervé Rouault <[email protected]>
2+
3+
* *: The ChangeLog is auto-generated when releasing. If you
4+
are seeing this, use 'git log' for a detailed list of changes.

‎LICENSE

+15
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,15 @@
1+
genherite - Evolutionary algorithm for the prediciton of genetic networks.
2+
3+
Copyright (C) 2005-2011 Hervé Rouault <[email protected]>
4+
5+
This program is free software: you can redistribute it and/or modify
6+
it under the terms of the GNU General Public License as published by
7+
the Free Software Foundation, either version 3 of the License, or
8+
(at your option) any later version.
9+
10+
This program is distributed in the hope that it will be useful,
11+
but WITHOUT ANY WARRANTY; without even the implied warranty of
12+
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13+
GNU General Public License for more details.
14+
15+
The included file 'COPYING' is a copy of the GNU General Public License.

‎Makefile.am

+47
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,47 @@
1+
#
2+
# Copyright (C) 2005-2011 Hervé Rouault <[email protected]>
3+
#
4+
# This file is part of Genherite.
5+
#
6+
# Genherite is free software: you can redistribute it and/or modify
7+
# it under the terms of the GNU General Public License as published by
8+
# the Free Software Foundation, either version 3 of the License, or
9+
# (at your option) any later version.
10+
#
11+
# Genherite is distributed in the hope that it will be useful,
12+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
13+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14+
# GNU General Public License for more details.
15+
#
16+
# You should have received a copy of the GNU General Public License
17+
# along with Genherite; see the file COPYING If not, see
18+
# <http://www.gnu.org/licenses/>.
19+
20+
ACLOCAL_AMFLAGS = -I m4
21+
22+
BUILT_SOURCES = $(top_srcdir)/.version
23+
24+
$(top_srcdir)/.version:
25+
echo $(VERSION) > $@-t && mv $@-t $@
26+
dist-hook:
27+
28+
29+
SUBDIRS = src doc
30+
31+
EXTRA_DIST = autogen.sh
32+
33+
dist-hook:
34+
echo $(VERSION) > $(distdir)/.tarball-version
35+
@if test -d "$(srcdir)/.git"; \
36+
then \
37+
echo Creating ChangeLog && \
38+
( cd "$(top_srcdir)" && \
39+
echo '# Generated by Makefile. Do not edit.'; echo; \
40+
$(top_srcdir)/missing --run git log --stat ) > ChangeLog.tmp \
41+
&& mv -f ChangeLog.tmp $(distdir)/ChangeLog \
42+
|| ( rm -f ChangeLog.tmp ; \
43+
echo Failed to generate ChangeLog >&2 ); \
44+
else \
45+
echo A git clone is required to generate a ChangeLog >&2; \
46+
fi
47+

‎NEWS

Whitespace-only changes.

‎README

+1
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
README.md

‎README.md

+23
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,23 @@
1+
Overview
2+
========
3+
4+
**Genherite** predicts genetic networks for multicellular cell fate decisions.
5+
6+
It is programmed in C/C++.
7+
8+
9+
Installation
10+
============
11+
12+
You can refer to the INSTALL file for detailled installation instructions.
13+
14+
Quick install
15+
-------------
16+
17+
```sh
18+
mkdir build
19+
cd build
20+
../configure
21+
make
22+
make install
23+
```

‎autogen.sh

+2
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
1+
#!/bin/sh
2+
autoreconf --force --install

‎configure.ac

+66
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,66 @@
1+
# genherite - Evolutionary algorithm for the prediciton of genetic networks.
2+
#
3+
# Copyright (C) 2005-2011 Hervé Rouault <[email protected]>
4+
#
5+
# This file is part of Genherite.
6+
#
7+
# Genherite is free software: you can redistribute it and/or modify
8+
# it under the terms of the GNU General Public License as published by
9+
# the Free Software Foundation, either version 3 of the License, or
10+
# (at your option) any later version.
11+
#
12+
# Genherite is distributed in the hope that it will be useful,
13+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
14+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15+
# GNU General Public License for more details.
16+
#
17+
# You should have received a copy of the GNU General Public License
18+
# along with Imogene; see the file COPYING If not, see
19+
# <http://www.gnu.org/licenses/>.
20+
#
21+
# -*- Autoconf -*-
22+
# Process this file with autoconf to produce a configure script.
23+
24+
AC_PREREQ([2.61])
25+
AC_INIT(Genherite, m4_esyscmd([tools/git-version-gen .tarball-version]),\
26+
[[email protected]])
27+
AM_INIT_AUTOMAKE()
28+
29+
AC_CONFIG_SRCDIR([src/genherite.cpp])
30+
AC_CONFIG_HEADERS([config.h])
31+
AC_CONFIG_MACRO_DIR([m4])
32+
m4_include([m4/ax_blas.m4])
33+
34+
# Checks for programs.
35+
AC_PROG_CXX
36+
AC_PROG_CC
37+
AM_PROG_CC_C_O
38+
39+
# Checks for libraries.
40+
AC_CHECK_LIB([m],[cos],,[AC_MSG_ERROR([math functions required.])])
41+
42+
##AX_BLAS( [ AC_MSG_NOTICE( [ blas libs variable : x$BLAS_LIBS BLAS_LIBS ] ) ], )
43+
AX_BLAS(LIBS="$BLAS_LIBS $LIBS $FLIBS", AC_CHECK_LIB([gslcblas],\
44+
[cblas_dgemm], , AC_MSG_ERROR([blas library required.])))
45+
46+
#AX_BLAS([],[AC_MSG_ERROR([blas library required.])])
47+
AC_CHECK_LIB([gsl],[gsl_blas_dgemm],,[AC_MSG_ERROR([libgsl required.])])
48+
49+
AC_CHECK_LIB(pthread,pthread_create)
50+
51+
# Checks for header files.
52+
AC_CHECK_HEADERS([gsl/gsl_rng.h],[],[AC_MSG_ERROR([gsl headers required.])])
53+
54+
# Checks for typedefs, structures, and compiler characteristics.
55+
AC_HEADER_STDBOOL
56+
57+
# Checks for library functions.
58+
AC_CHECK_FUNCS([floor pow sqrt], [],\
59+
[AC_MSG_ERROR([floor,pow and sqrt functions required])])
60+
61+
62+
AC_CONFIG_FILES([Makefile
63+
doc/Makefile
64+
src/Makefile])
65+
66+
AC_OUTPUT

‎doc/Makefile.am

+23
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,23 @@
1+
#
2+
# Copyright (C) 2005-2011 Hervé Rouault <[email protected]>
3+
#
4+
# This file is part of Genherite.
5+
#
6+
# Genherite is free software: you can redistribute it and/or modify
7+
# it under the terms of the GNU General Public License as published by
8+
# the Free Software Foundation, either version 3 of the License, or
9+
# (at your option) any later version.
10+
#
11+
# Genherite is distributed in the hope that it will be useful,
12+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
13+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14+
# GNU General Public License for more details.
15+
#
16+
# You should have received a copy of the GNU General Public License
17+
# along with Genherite; see the file COPYING If not, see
18+
# <http://www.gnu.org/licenses/>.
19+
20+
AM_MAKEINFOHTMLFLAGS = --no-split
21+
22+
info_TEXINFOS = genherite.texi
23+
genherite_TEXINFOS = fdl.texi

0 commit comments

Comments
 (0)