Tutorial:Getting Cegma/Genewise To Work On Centos, Rhel

Question

[Adrian Pelin]

# 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.

[Hranjeev]

This is a god-send :) Thank you!

[Buttonwood]

Does anyone know how to install genewise on a redhat OS server?

[Adrian Pelin]

above you is the exact tutorial on how to do it.

[Buttonwood]

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!

[Adrian Pelin]

have you also done "sudo yum install glib-devel"?

[Buttonwood]

Yes, I also done sudo yum install glib-devel but there is no such package;

so I did

find ./ -name make |xargs sed -i 's/glib-config/pkg-config --libs glib-2.0/'

and it seems work.

Thank you.

Darked89: ake changed to make

Answer 1

[Darked89]

re getting wise2.4.1:

1. it exist as Debian package: https://packages.debian.org/unstable/science/wise
   • sudo apt-get install wise

2. 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.