archive:bioinformatic_tools:abyss
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision | Next revision Both sides next revision | ||
|
archive:bioinformatic_tools:abyss [2010/04/15 19:34] galt |
archive:bioinformatic_tools:abyss [2010/04/28 23:41] cbrumbau Updated with install instructions |
||
|---|---|---|---|
| Line 9: | Line 9: | ||
| ==== Installing ==== | ==== Installing ==== | ||
| - | cd /campusdata/BME235/programs | + | Get the appropriate source files to be compiled: |
| - | wget http://www.bcgsc.ca/downloads/abyss/abyss-1.1.2.tar.gz | + | |
| - | tar xfz abyss-1.1.2.tar.gz | + | |
| - | mv abyss-1.1.2 abyss | + | |
| - | mv abyss-1.1.2.tar.gz abyss/ | + | |
| - | cd abyss | + | |
| + | <code> | ||
| + | cd /campusdata/BME235/programs | ||
| + | wget http://www.bcgsc.ca/downloads/abyss/abyss-1.1.2.tar.gz | ||
| + | wget http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.1.tar.gz | ||
| + | wget http://google-sparsehash.googlecode.com/files/sparsehash-1.7.tar.gz | ||
| + | tar xfz abyss-1.1.2.tar.gz | ||
| + | tar xfz openmpi-1.4.1.tar.gz | ||
| + | tar xfz sparsehash-1.7.tar.gz | ||
| + | mv abyss-1.1.2.tar.gz abyss-1.1.2/ | ||
| + | mv openmpi-1.4.1.tar.gz openmpi-1.4.1/ | ||
| + | mv sparsehash-1.7.tar.gz sparsehash-1.7/ | ||
| + | </code> | ||
| - | Still need to check out Google sparsehash, | + | First, OpenMPI and Google sparsehash need to be compiled and installed for ABySS. |
| - | and where openmpi libs are installed. | + | |
| - | Have not run configure and make. | + | |
| - | Possilby the make install will require sudo, | + | |
| - | judging by the example. | + | |
| + | <code> | ||
| + | cd /campusdata/BME235/programs/openmpi-1.4.1 | ||
| + | ./configure --prefix=/campusdata/BME235 | ||
| + | make | ||
| + | make install | ||
| + | cd /campusdata/BME235/programs/sparsehash-1.7 | ||
| + | ./configure --prefix=/campusdata/BME235 | ||
| + | make | ||
| + | make install | ||
| + | </code> | ||
| - | ==== Website ==== | + | Next, a [[http://code.google.com/p/google-sparsehash/issues/detail?id=55|patch]] needs to be applied so that ABySS can properly compile with support for Google sparsehash 1.7. This issue will be fixed in the next release of Google sparsehash. |
| - | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss]] | + | |
| - | ==== Source with Binaries and Documentation ==== | + | <code> |
| - | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases]] | + | cd /campusdata/BME235/include/google/sparsehash |
| + | wget http://google-sparsehash.googlecode.com/issues/attachment?aid=-5666329961626930947&name=deallocate.diff | ||
| + | patch < deallocate.diff | ||
| + | </code> | ||
| + | |||
| + | Now ABySS can be compiled with OpenMPI and Google sparsehash support. | ||
| + | |||
| + | <code> | ||
| + | cd /campusdata/BME235/programs/abyss-1.1.2 | ||
| + | ./configure --prefix=/campusdata/BME235 CPPFLAGS=-I/campusdata/BME235/include | ||
| + | make | ||
| + | make install | ||
| + | </code> | ||
| + | |||
| + | ==== Websites ==== | ||
| + | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss|ABySS]] \\ | ||
| + | [[http://www.open-mpi.org|OpenMPI]] \\ | ||
| + | [[http://code.google.com/p/google-sparsehash|Google sparsehash]] | ||
| + | |||
| + | ==== Sources with Binaries and Documentation ==== | ||
| + | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases|ABySS]] \\ | ||
| + | [[http://www.open-mpi.org/software/ompi|OpenMPI]] \\ | ||
| + | [[http://code.google.com/p/google-sparsehash/downloads/list|Google sparsehash]] | ||
| ===== References ===== | ===== References ===== | ||
archive/bioinformatic_tools/abyss.txt · Last modified: 2015/07/28 06:23 by ceisenhart
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
