libgcc_s.so.1 must be installed for pthread_cancel to work

# /BiO/apps/interproscan-5.7-48.0/bin/blast/2.2.6/blastall -p blastp -F F -e 0.0005 -b 300 -v 300 -m 8 -a 4 -d /BiO/apps/interproscan-5.7-48.0/data/pirsf/2.84/sf.seq -i /BiO/scratch/biosysrnd/firefox/RESEARCH/Prometheus/Rawdata/TheOthers/Picea_abies/temp/ngs-0-1.local_20161103_195224381_jvqw/jobPIRSF-2.84/000000000951_000000001000.blastInputFile.fasta
libgcc_s.so.1 must be installed for pthread_cancel to work


# yum whatprovides libgcc_s.so.1
# yum install libgcc-4.4.7-11.el6.i686

Galaxy

https://galaxyproject.org/

# service mysqld start

# /usr/bin/mysql_secure_installation

# /usr/bin/mysql -u root -p

mysql> INSERT INTO mysql.user (User,Host,Password) VALUES('galaxy','localhost',PASSWORD('password'));

mysql> FLUSH PRIVILEGES;

mysql> CREATE DATABASE galadb;

mysql> GRANT ALL PRIVILEGES ON galadb.* to galaxy@localhost;

mysql> FLUSH PRIVILEGES;

mysql> quit

# cd /usr/local

# mkdir galaxy

# cd galaxy/

# hg clone https://bitbucket.org/galaxy/galaxy-dist/

# cd galaxy-dist 

# vi config/galaxy.ini

debug = True –> debug = False

use_interactive = True –>  use_interactive = False

database_connection = mysql://galaxy:password@localhost/galadb?unix_socket=/var/lib/mysql/mysql.sock

use_threadpool = true

threadpool_workers = 7

start_job_runners = drmaa

environment_setup_file = True

default_cluster_job_runner = drmaa://-V/

# sh run.sh

INSTALLING BOOST LIBRARIES, TOPHAT, SAM TOOLS, CUFFLINKS ON CENTOS7

Boost Libraries

$ tar zxvfp boost_1_62_0.tar.gz

$ cd boost_1_62_0/

$ ./bootstrap.sh --prefix=/BiO/hadoop/program/linux_tools/boost_1_62_0 --with-libraries=all

$ ./b2

$ ./b2 install

$ export BOOST_ROOT=/BiO/hadoop/program/linux_tools/boost_1_62_0

$ export LD_LIBRARY_PATH=$BOOST_ROOT/lib:$LD_LIBRARY_PATH

TopHat

$ tar xzvf tophat-2.1.1.tar.gz

$ cd tophat-2.1.1

$ ./configure --prefix /BiO/hadoop/program/linux_tools/tophat-2.1.1 \
 --with-boost=/BiO/hadoop/program/linux_tools/boost_1_62_0

$ make

$ sudo make install

SAM tools

$ cd samtools-0.1.19/ 

$ make

$ mkdir -p /BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19/bin  \
/BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19/include/bam \
/BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19/lib \

$ cp libbam.a /BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19/lib/

$ cp *.h /BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19/include/bam/

Cufflinks

$ tar jxfp 3.2.8.tar.bz2

$ cd eigen-eigen-07105f7124f9/

$ mkdir /BiO/hadoop/program/linux_tools/isbyeon_test/eigen3

$ cp -rv ./Eigen/ /BiO/hadoop/program/linux_tools/isbyeon_test/eigen3

$ export EIGEN_CPPFLAGS="-I/BiO/hadoop/program/linux_tools/isbyeon_test/eigen3"

$ tar zxvfp cufflinks-2.2.1.tar.gz

$ cd cufflinks-2.2.1/

$ ./configure --prefix=//BiO/hadoop/program/linux_tools/isbyeon_test/cufflinks-2.2.1 \
--with-boost=/BiO/hadoop/program/linux_tools/boost_1_62_0 \
--with-bam=/BiO/hadoop/program/linux_tools/isbyeon_test/samtools-0.1.19

$ make

$ make install