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maker-software [2021/07/07 06:46]
aorth
maker-software [2021/11/01 09:11] (current)
aorth
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 $ maker -h</code> $ maker -h</code>
  
-**Note:** Maker generates literally millions of small files. Please please please make sure you direct your program output to the local ''/var/scratch'' directory on the compute node where your job is running. Your job will run much faster and will not burden the network file system on ''/home''.+**Note 1:** Maker generates literally millions of small files. Please please please make sure you direct your program output to the local ''/var/scratch'' directory on the compute node where your job is running. Your job will run much faster and will not burden the network file system on ''/home''
 + 
 +**Note 2:** Maker uses a lot of temporary storage in ''/tmp'' by default. Please make sure to use something like ''-TMP /var/scratch'' to use a more appropriate location.
  
 ===== Installation ====== ===== Installation ======
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 $ wget https://hpc.ilri.cgiar.org/mirror/centos/7/os/x86_64/Packages/centos-release-7-9.2009.0.el7.centos.x86_64.rpm $ wget https://hpc.ilri.cgiar.org/mirror/centos/7/os/x86_64/Packages/centos-release-7-9.2009.0.el7.centos.x86_64.rpm
 $ sudo rpm --root=/var/tmp/chroot/maker -i centos-release-7-9.2009.0.el7.centos.x86_64.rpm $ sudo rpm --root=/var/tmp/chroot/maker -i centos-release-7-9.2009.0.el7.centos.x86_64.rpm
-$ sudo yum --installroot=/var/tmp/chroot/maker install -y rpm-build yum gcc wget vim perl perl-App-cpanminus.noarch expat-devel mpich-3.2.x86_64+$ sudo yum --installroot=/var/tmp/chroot/maker install -y rpm-build yum gcc wget vim perl perl-App-cpanminus.noarch expat-devel
 $ sudo cp /etc/resolv.conf /var/tmp/chroot/maker/etc $ sudo cp /etc/resolv.conf /var/tmp/chroot/maker/etc
 $ sudo mount --bind /dev/ /var/tmp/chroot/maker/dev $ sudo mount --bind /dev/ /var/tmp/chroot/maker/dev
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 # cp -r maker/* /export/apps/maker/3.01.03 # cp -r maker/* /export/apps/maker/3.01.03
 # cd /export/apps/maker/3.01.03/src # cd /export/apps/maker/3.01.03/src
-# Check dependencies that need satisfying...+# Check Perl dependencies that need satisfying...
 # perl Build.PL # perl Build.PL
 # cpanm -l /export/apps/maker/3.01.03/deps DBD::SQLite # cpanm -l /export/apps/maker/3.01.03/deps DBD::SQLite
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 $ perl Build.PL $ perl Build.PL
 $ module load repeatmasker/4.1.1 snap/2013-11-29 exonerate/2.2.0 augustus/3.2.3 $ module load repeatmasker/4.1.1 snap/2013-11-29 exonerate/2.2.0 augustus/3.2.3
 +# change permissions on this table of contents that Maker's build script wants to touch:
 +$ sudo chown -R aorth:aorth /export/apps/perl/5.16.3.1603/html/perltoc.html
 +# install mpich-3.2-devel so we can get mpicc to enable MPI support in Maker
 +$ sudo yum install mpich-3.2-devel.x86_64
 $ perl Build.PL $ perl Build.PL
 $ ./Build install $ ./Build install
maker-software.1625640406.txt.gz · Last modified: 2021/07/07 06:46 by aorth