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--- archive:bioinformatic_tools:abyss [2010/05/10 23:15]
jstjohn
+++ archive:bioinformatic_tools:abyss [2010/05/11 04:32]
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>
+the installation crashed due to a warning (-Werror was enabled). I modified configure.ac so that it is no longer enabled:
+<code>
+#AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra -Werror')
+AC_SUBST(AM_CXXFLAGS, '-Wall -Wextra')
+</code>
+Next I run autoconf to work with the modified configure.ac file:
+<code>
+/campus/BME235/bin/autoconf/bin/autoreconf
+/campus/BME235/bin/autoconf/bin/autoconf
+</code>
+Finally I re-do the configure, and install:
+<code>
+./configure --prefix=/campusdata/BME235/programs/abyss_tmp/ CPPFLAGS='-I/opt/openmpi/include -I/campusdata/BME235/include'  --with-mpi=/opt/openmpi
+make -j8 install
+cd ../
+fixmode . &
+</code>
 ==== Websites ====
@@ Line 72: / Line 108: @@
 ===== Slug Assembly =====
+====Attempt1====
 In the directory:
   /campus/BME235/assemblies/slug/ABySS-assembly1
@@ Line 90: / Line 128: @@
 Unfortunately this command crashes. The error states that the LD_LIBRARY_PATH might need to be set to point to shared MPI libraries. Also it would probably be best to use our version of "mpirun" once we get it compiled with sge support.
+====Attempt 2====
+I modified the script to use the other parallel version of ABySS I installed as described above, attempted in the same directory since the last attempt was entirely unsuccessfull:
+<code>
+/campus/BME235/assemblies/slug/ABySS-assembly1/run1_abyss_mpi.sh:
+#!/bin/bash
+#
+#$ -cwd
+#$ -j y
+#$ -S /bin/bash
+#$ -V
+#$ -l mem_free=15g
+#
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/openmpi/lib:/campus/BME235/lib
+#make the new MPI version of abyss prioritized
+export PATH=/campus/BME235/programs/abyss_tmp/bin:$PATH/opt/openmpi/bin/mpirun -np $NSLOTS abyss-pe -j j=2 np=$NSLOTS n=8 k=25 name=slugAbyss lib='lane1 lane2 lane3 lane5 lane6 lane7 lane8' lane1='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_1_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_1_2_all_qseq.fastq' lane2='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_2_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_2_2_all_qseq.fastq' lane3='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_3_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_3_2_all_qseq.fastq' lane5='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_5_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_5_2_all_qseq.fastq' lane6='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_6_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_6_2_all_qseq.fastq' lane7='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_7_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_7_2_all_qseq.fastq' lane8='/campus/BME235/data/slug/I
+llumina/illumina_run_1/CeleraReads/s_8_1_all_qseq.fastq  /campus/BME235/data/slug/Illumina/illumina_
+run_1/CeleraReads/s_8_2_all_qseq.fastq'
+</code>
+And I run the script using the following qsub command:
+<code>
+qsub -pe orte 40 run1_abyss_mpi.sh
+</code>
 ===== References =====
 <refnotes>notes-separator: none</refnotes>
 ~~REFNOTES cite~~

Banana Slug Genomics

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