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maker-software [2021/07/07 07:22]
aorth
maker-software [2021/11/01 09:11] (current)
aorth
Line 19: Line 19:
 $ 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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 $ rsync -av /var/tmp/chroot/maker/export/apps/maker/3.01.03/ /export/apps/maker/3.01.03 $ rsync -av /var/tmp/chroot/maker/export/apps/maker/3.01.03/ /export/apps/maker/3.01.03
 $ cd /export/apps/maker/3.01.03/src $ cd /export/apps/maker/3.01.03/src
-$ sudo yum install mpich-3.2-devel.x86_64 
 $ export PERL5LIB="/export/apps/maker/3.01.03/deps/lib/perl5" $ export PERL5LIB="/export/apps/maker/3.01.03/deps/lib/perl5"
 # Check that all Perl dependencies are satisfied... # Check that all Perl dependencies are satisfied...
 $ 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.1625642522.txt.gz · Last modified: 2021/07/07 07:22 by aorth