archive:bioinformatic_tools:abyss
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archive:bioinformatic_tools:abyss [2010/05/20 20:48] jstjohn |
archive:bioinformatic_tools:abyss [2015/07/28 06:23] (current) ceisenhart ↷ Page moved from bioinformatic_tools:abyss to archive:bioinformatic_tools:abyss |
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| </code> | </code> | ||
| + | === Yet Another Install (1.2.7) === | ||
| + | |||
| + | On 7 Jun 2011, Kevin Karplus tried installing abyss-1.2.7 from /campusdata/BME235/programs/abyss-1.2.7/ using | ||
| + | |||
| + | <code> | ||
| + | configure --prefix=/campusdata/BME235 \ | ||
| + | CPPFLAGS='-I/opt/openmpi/include -I/campusdata/BME235/include' \ | ||
| + | LDFLAGS=-L/campusdata/BME235/lib \ | ||
| + | CC=gcc44 CXX=g++44 \ | ||
| + | --with-mpi=/opt/openmpi | ||
| + | </code> | ||
| + | |||
| + | Before this configure could work, sparsehash-1.10 was installed from /campusdata/BME235/programs/google/sparsehash-1.10/ | ||
| ==== Websites ==== | ==== Websites ==== | ||
| [[http://www.bcgsc.ca/platform/bioinfo/software/abyss|ABySS]] \\ | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss|ABySS]] \\ | ||
| [[http://www.open-mpi.org|OpenMPI]] \\ | [[http://www.open-mpi.org|OpenMPI]] \\ | ||
| - | [[http://code.google.com/p/google-sparsehash|Google sparsehash]] | + | [[http://code.google.com/p/google-sparsehash|Google sparsehash]] \\ |
| + | [[http://www.boost.org/|Boost]] | ||
| ==== Sources with Binaries and Documentation ==== | ==== Sources with Binaries and Documentation ==== | ||
| [[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases|ABySS]] \\ | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases|ABySS]] \\ | ||
| [[http://www.open-mpi.org/software/ompi|OpenMPI]] \\ | [[http://www.open-mpi.org/software/ompi|OpenMPI]] \\ | ||
| - | [[http://code.google.com/p/google-sparsehash/downloads/list|Google sparsehash]] | + | [[http://code.google.com/p/google-sparsehash/downloads/list|Google sparsehash]] \\ |
| + | [[http://www.boost.org/users/history/version_1_57_0.html|Boost]] | ||
| ===== Slug Assembly ===== | ===== Slug Assembly ===== | ||
| Line 244: | Line 257: | ||
| Campusrocks-0-6.local is back up so I am re-starting this task. At its peak the KAligner step (where it crashed previously when the -j option was enabled) requires quite a lot of ram. I am hoping that the 30GB available on this node is sufficient. | Campusrocks-0-6.local is back up so I am re-starting this task. At its peak the KAligner step (where it crashed previously when the -j option was enabled) requires quite a lot of ram. I am hoping that the 30GB available on this node is sufficient. | ||
| - | |||
| ====Attempt 4==== | ====Attempt 4==== | ||
| I have access to kolossus which has 1.1tb of ram. I will now run the program on kolossus to see if it will assemble there... | I have access to kolossus which has 1.1tb of ram. I will now run the program on kolossus to see if it will assemble there... | ||
| Line 286: | Line 298: | ||
| |gzip >lib1-3.pair.gz | |gzip >lib1-3.pair.gz | ||
| </code> | </code> | ||
| + | |||
| + | This step takes a lot of time. After running for approximately 24 hours it finally finished, and then when I tried to restart the makefile I accidently executed the previous KAligner command and the lib1-3.pair.gz file was written over... For now I am going to let the Ray assembly finish on Kolossus, and then I will re-run this step. Note that since campusrocks-0-6.local is back online I am also re-trying this stage in "Attempt 3" above. Since the run on campusrocks is split up between the 7 lanes rather than one large run, it is possible that it will work even with limited ram. One of the selling points of ABySS is that it is supposed to run on "commodity hardware" so we will see if it lives up to that claim. | ||
archive/bioinformatic_tools/abyss.1274388532.txt.gz · Last modified: 2010/05/20 20:48 by jstjohn
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