From d541a78ec298dac65960ce90b47cef84eb951ce4 Mon Sep 17 00:00:00 2001 From: noe Date: Thu, 22 Jun 2023 14:42:06 +0200 Subject: [PATCH 1/2] Updating bioinfo.cristal.univ-lille.fr to bioinfo.univ-lille.fr --- README | 2 +- README.rst | 12 ++++++------ configure | 6 +++--- configure.ac | 2 +- src/main.cc | 4 ++-- tests/iedera_gcov_test3 | 2 +- 6 files changed, 14 insertions(+), 14 deletions(-) diff --git a/README b/README index d08727c..1abfafe 100644 --- a/README +++ b/README @@ -5,7 +5,7 @@ tool is implemented in C++ and provided for research purposes only. Help on this program can be obtained with the --help (-h) parameter, or from the homepage : - http://bioinfo.cristal.univ-lille.fr/yass/iedera.php + http://bioinfo.univ-lille.fr/yass/iedera.php Several specific examples and papers are also provided on this webpage, depending on the specific usage you would need. diff --git a/README.rst b/README.rst index 4a84d96..634d702 100644 --- a/README.rst +++ b/README.rst @@ -10,15 +10,15 @@ :target: https://app.codecov.io/gh/laurentnoe/iedera/branch/master :alt: Coverage -.. image:: https://img.shields.io/website.svg?style=flat-square&label=Website&url=https%3A%2F%2Fbioinfo.cristal.univ-lille.fr - :target: https://bioinfo.cristal.univ-lille.fr/yass/iedera.php +.. image:: https://img.shields.io/website.svg?style=flat-square&label=Website&url=https%3A%2F%2Fbioinfo.univ-lille.fr + :target: https://bioinfo.univ-lille.fr/yass/iedera.php :alt: Website iedera ====== -(more at ) +(more at ) ``iedera`` is a tool to select and design *spaced seeds*, *transition constrained spaced seeds*, or more generally *subset seeds*, and @@ -28,7 +28,7 @@ constrained spaced seeds*, or more generally *subset seeds*, and Installation ------------ -(more at ) +(more at ) Binaries for Windows (x64) and OS X (x64) are available at . @@ -66,7 +66,7 @@ or copy the binary directly to your homedir:: Command-line ------------ -(more at ) +(more at ) **First, use** one of these two parameters : @@ -114,7 +114,7 @@ consider the two following: to activate the hill-climbing algorithm on previous parameter -r -(more at ) +(more at ) Examples diff --git a/configure b/configure index 27a666e..e5ee047 100755 --- a/configure +++ b/configure @@ -613,7 +613,7 @@ PACKAGE_TARNAME='iedera' PACKAGE_VERSION='1.07' PACKAGE_STRING='iedera 1.07' PACKAGE_BUGREPORT='laurent DT noe AT univ-lille DT fr' -PACKAGE_URL='http://bioinfo.cristal.univ-lille.fr/yass/iedera' +PACKAGE_URL='http://bioinfo.univ-lille.fr/yass/iedera' ac_unique_file="src/main.cc" # Factoring default headers for most tests. @@ -1396,7 +1396,7 @@ Use these variables to override the choices made by `configure' or to help it to find libraries and programs with nonstandard names/locations. Report bugs to . -iedera home page: . +iedera home page: . _ACEOF ac_status=$? fi @@ -4789,7 +4789,7 @@ Configuration commands: $config_commands Report bugs to . -iedera home page: ." +iedera home page: ." _ACEOF ac_cs_config=`printf "%s\n" "$ac_configure_args" | sed "$ac_safe_unquote"` diff --git a/configure.ac b/configure.ac index 387f2cd..aea8889 100644 --- a/configure.ac +++ b/configure.ac @@ -181,7 +181,7 @@ AC_DEFUN([ACX_CHECK_TYPE_TRAITS_CXX11], [ -AC_INIT([iedera],[1.07],[laurent DT noe AT univ-lille DT fr],[iedera],[http://bioinfo.cristal.univ-lille.fr/yass/iedera]) +AC_INIT([iedera],[1.07],[laurent DT noe AT univ-lille DT fr],[iedera],[http://bioinfo.univ-lille.fr/yass/iedera]) AC_CONFIG_SRCDIR([src/main.cc]) AC_LANG([C++]) AM_INIT_AUTOMAKE([subdir-objects diff --git a/src/main.cc b/src/main.cc index 86f895d..3481cc4 100644 --- a/src/main.cc +++ b/src/main.cc @@ -11,7 +11,7 @@ * * @section Download * Download the iedera source code and binaries on the following web page:\n - * http://bioinfo.cristal.univ-lille.fr/yass/iedera.php\n + * http://bioinfo.univ-lille.fr/yass/iedera.php\n * A small tutorial to use iedera is also provided on this web page.\n * * @author Laurent Noe @@ -420,7 +420,7 @@ void USAGE() { cerr << " -b ,,... : set the Bernoulli/Markov background distribution (size |'A'|^k)" << endl; cerr << " -f ,,... : set the Bernoulli/Markov foreground distribution (size |'A'|^k)" << endl; cerr << " -fF : set the foreground model (as a probabilistic NFA)" << endl; - cerr << " for more details, see http://bioinfo.cristal.univ-lille.fr/yass/iedera.php#fFFormat" << endl; + cerr << " for more details, see http://bioinfo.univ-lille.fr/yass/iedera.php#fFFormat" << endl; cerr << " -l : set the alignment length (default = " << gv_alignment_length << ") " << endl; cerr << " -ll : select the sub-align window computation and set its length (default = disabled)" << endl; cerr << " -llf : set the sub-align function used to merge the results (default = \"min\")" << endl; diff --git a/tests/iedera_gcov_test3 b/tests/iedera_gcov_test3 index 9c95cf6..61acc99 100755 --- a/tests/iedera_gcov_test3 +++ b/tests/iedera_gcov_test3 @@ -1,5 +1,5 @@ #!/bin/sh -# the protein non-tree-transitive from http://bioinfo.cristal.univ-lille.fr/yass/iedera_proteins/Makefile.sh +# the protein non-tree-transitive from https://bioinfo.univ-lille.fr/yass/iedera_proteins/Makefile.sh ./iedera_gcov -z 1 -w 3,6 -j 0.05 -n 2 -r 100 -k -l 16 -s 1,7 -A 47 -B 22 -M \{\{1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{1,1,1,1,1,0,0,0,1,0,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{0,1,1,1,1,0,1,1,0,1,0,1,1,1,0,0,1,1,0,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,1,0,1,1,0,0,0,0,0,0,0,1,0,1,1,1,1,0,1,0,1,1,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1\},\{0,0,0,1,1,0,0,1,0,1,1,0,1,1,0,1,0,1,1,0,0,0,0,1,0,0,1,1,0,0,1,1,0,1,1,1,0,1,1,1,1,1,1,0,1,1,1\},\{0,0,0,0,0,1,1,1,1,0,1,1,1,1,1,0,1,1,1,1,0,1,1,1,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,1,1,1,0,0,1,1,0,1,1,0,1,1,0,1,1,0,1,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,1,1,0,0,1,1,1,1,0,0,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,0,0,0,0,0,1,1,0,0,0,1,1,0,1,0,1,1,0,1,1,1,1,1,1,1,0,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,1,1,1,0,1,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,0,0,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,1,0,0,1,0,1,1,0,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,1,0,1,1,0,1,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,1,1,1,0,1,1,1,1,1,1,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,1,1,1,1,0,1,1,1,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,1,1,1,0,1,1,0,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,1,0,0,1,0,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1\},\{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1\}\} -f 0.01612,0.01412,0.02288,0.00065,0.14347,0.00154,0.00168,0.01030,0.01514,0.01052,0.01076,0.01056,0.00419,0.00591,0.00192,0.00081,0.02840,0.05675,0.00273,0.00330,0.00029,0.01035,0.00191,0.03588,0.00030,0.02367,0.00466,0.00046,0.02768,0.00072,0.00759,0.01365,0.00286,0.01994,0.00964,0.00210,0.00983,0.04172,0.01117,0.00940,0.00744,0.00986,0.03641,0.00347,0.00708,0.00848,0.33169 -b 0.05108,0.03647,0.06770,0.00256,0.27712,0.00366,0.00485,0.01880,0.02941,0.01701,0.01457,0.01731,0.00757,0.00956,0.00389,0.00193,0.03584,0.07233,0.00571,0.00690,0.00064,0.01405,0.00281,0.04220,0.00068,0.02704,0.00418,0.00129,0.03316,0.00190,0.00860,0.01192,0.00234,0.01605,0.00704,0.00180,0.00583,0.02786,0.00752,0.00583,0.00479,0.00494,0.01591,0.00208,0.00372,0.00306,0.05849 || exit 99 ./iedera_gcov -z 1 -j 0.05 -l 16 -A 64 -B 64 -m "#53;v3R,L34K" || exit 99 From 5e14d135557ca581d99458dae2dc1612c3ca66df Mon Sep 17 00:00:00 2001 From: noe Date: Thu, 22 Jun 2023 14:48:09 +0200 Subject: [PATCH 2/2] Updating bioinfo.cristal.univ-lille.fr to bioinfo.univ-lille.fr : minor redirect issue --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 634d702..d8b4738 100644 --- a/README.rst +++ b/README.rst @@ -10,7 +10,7 @@ :target: https://app.codecov.io/gh/laurentnoe/iedera/branch/master :alt: Coverage -.. image:: https://img.shields.io/website.svg?style=flat-square&label=Website&url=https%3A%2F%2Fbioinfo.univ-lille.fr +.. image:: https://img.shields.io/website.svg?style=flat-square&label=Website&url=http%3A%2F%2F193.54.101.81%2Fyass%2F :target: https://bioinfo.univ-lille.fr/yass/iedera.php :alt: Website