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--- archive:bioinformatic_tools:abyss [2010/05/10 23:15]
jstjohn
+++ archive:bioinformatic_tools:abyss [2010/05/11 03:56]
jstjohn
@@ Line 13: / Line 13: @@
 Note that ABySS is also the recommended assembler by Illumina for large genomes. {{:bioinformatic_tools:abyss_technote_illumina.pdf|Illumina Technote Paper}}
 ==== Installing ====
@@ Line 60: / Line 59: @@
 make install
 </code>
+=== Alternate Install ===
+Attempt installing against campusdata's openmpi which is already configured to work with SGE. Note to force inclusion of the correct mpi.h file I specify the include path to the
+<code>
+cd /campusdata/BME235/programs/abyss_tmp/abyss-1.1.2
+./configure --prefix=/campusdata/BME235/programs/abyss_tmp/ CPPFLAGS='-I/opt/openmpi/include -I/campusdata/BME235/include'  --with-mpi=/opt/openmpi
+</code>
+Next i qlogin into some node and run make install in parallel:
+<code>
+qlogin
+make -j8 install
+</code>
 ==== Websites ====

Banana Slug Genomics