# This is based on a Ubuntu guide:
http://korflab.ucdavis.edu/datasets/cegma/ubuntu_instructions_1.txt
# get these
ftp://genome.crg.es/pub/software/geneid/geneid_v1.4.4.Jan_13_2011.tar.gz
ftp://selab.janelia.org/pub/software/hmmer3/3.0/hmmer-3.0.tar.gz
http://korflab.ucdavis.edu/Datasets/cegma/cegma_v2.4.010312.tar.gz
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.25+-x64-linux.tar.gz
http://ftp-stud.hs-esslingen.de/ubuntu/pool/universe/w/wise/wise_2.4.1.orig.tar.gz
# Genewise install
# need this to avoid glib-config error in genewise install
sudo yum install glib
sudo yum install glib-devel
cd wise2.4.1/src
# modify makefile to use "CC = cc" into "CC = gcc"
cd wise2.4.1/src/HMMer2/
sed 's/getline/getline_new/' sqio.c > a && mv a sqio.c
# that takes care of a get line error
cd ../models/
# Change phasemodel.c
From:
if( !isnumber(line[0]) ) {
To:
if( !isdigit(line[0]) ) {
# That takes care of a isnumber error
# Genewise install is the most problematic one, the rest install flawlessly.
# I thought I would start from the Ubuntu guide and change what is needed for CentOS.Turns out the glib part is slightly different, the rest is the same.
re getting wise2.4.1:
- it exist as Debian package: https://packages.debian.org/unstable/science/wise
- sudo apt-get install wise
if you are not on Debian/Ubuntu, you will be better of getting wise_2.4.1-17.debian.tar.xz from the above Debian wise package page, unpacking it and applying to wise-2.4.1 from wise_2.4.1.orig.tar.gz by running:
for file in debian/patches/[01]*.patch; do patch -p0 < $file; done
CAVEAT:
No idea why, but 10_fix_path_to_data_files.patch has different directory naming. Quick and dirty way of fixing it is to softlink wise-2.4.1 to b:
ln -s wise-2.4.1 b
Then everything compiled with gcc_4.8.1 without problems.
Does anyone know how to install genewise on a redhat OS server?
above you is the exact tutorial on how to do it.
Thanks you very much
But I still need your help
I followed your steps
but get these:
make CC="gcc" CFLAGS="-c -O3 `glib-config --cflags`" libwisebase.a )
/bin/sh: glib-config: command not found
if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi
make[1]: Leaving directory `/data/tanhao/dev/gene_prediction/GeneWise/wise-2.4.1/src/dynlibsrc'
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O3`glib-config --cflags`" libdyna_glib.a )
/bin/sh: glib-config: command not found
make[1]: Entering directory `/data/tanhao/dev/gene_prediction/GeneWise/wise-2.4.1/src/dynlibsrc'
I have done sudo yum install glib
Then I searched “/bin/sh: glib-config: command not found” and followed the seqanswer's tips: http://seqanswers.com/forums/showthread.php?t=24027
to edit the makefile and change
CFLAGS = -c -O3 `glib-config --cflags`
to
CFLAGS = -c -O3 `pkg-config --libs glib-2.0 --cflags`
But I still get errors like:
(cd network ; make CC="gcc" CFLAGS="-c -O3 `pkg-config --libs glib-2.0 --cflags`" all )
make[1]: Entering directory `/data/tanhao/dev/gene_prediction/GeneWise/wise-2.4.1/src/network'
gcc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c
gcc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c
gcc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm`glib-config --libs`-lpthread
/bin/sh: glib-config: command not found
../dynlibsrc/libdyna_glib.a(subseqhash.o): In function`Wise2_is_populated_subseqhash_ghash':
subseqhash.c:(.text+0x18): undefined reference to `g_hash_table_lookup'
../dynlibsrc/libdyna_glib.a(subseqhash.o): In function`Wise2_add_direct_number_subseqhash_ghash':
subseqhash.c:(.text+0x7a): undefined reference to `g_hash_table_lookup'
subseqhash.c:(.text+0xc2): undefined reference to `g_hash_table_insert'
../dynlibsrc/libdyna_glib.a(subseqhash.o): In function `Wise2_add_seq_subseqhash_ghash':
subseqhash.c:(.text+0x138): undefined reference to `g_hash_table_lookup'
subseqhash.c:(.text+0x17a): undefined reference to `g_hash_table_insert'
../dynlibsrc/libdyna_glib.a(subseqhash.o): In function `Wise2_lookup_subseqhash_ghash':
subseqhash.c:(.text+0x1b8): undefined reference to `g_hash_table_lookup'
It seems the glib-config problem is still there!
Do you have any suggestion for me?And thank you again!
This is a god-send :) Thank you!