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--- archive:bioinformatic_tools:allpaths [2010/04/07 09:23]
jstjohn
+++ archive:bioinformatic_tools:allpaths [2010/04/19 05:14]
jstjohn
@@ Line 1: / Line 1: @@
 ===== ALLPATHS =====
-Attached is the Allpaths3 version 1.0 documentation converted from .docx format to .pdf. You can download this file by clicking the following link: {{:bioinformatic_tools:allpathsv3_manual_r1.0.pdf|allpathsv3_manual_r1.0.pdf}}.
+Attached is the Allpaths3 version 1.0 documentation converted from .docx format to .pdf. You can download this file by clicking the following link: {{:bioinformatic_tools:allpathsv3_manual_r1.0_2.pdf|allpathsv3_manual}}.
 ====Potential Pitfalls====
-Designed to work with 100+ bp paired end reads from a *minimum of one short and one long set of libraries. Also the program expects 40X coverage from each of those libraries! Additionally they say it requires a minimum of 32Gb of ram, but for a full sized mammalian genome they recommend 512Gb of ram!! I assume they mean shared memory here so this program may be a no go. I am building the program but stopping short of installing it due to these limitations.
+Designed to work with 100+ bp paired end reads from a *minimum of one short and one long set of libraries. Also the program expects 40X coverage from each of those libraries! Additionally they say it requires a minimum of 32Gb of ram which I assume means shared memory, so it may not work on our cluster. Maybe it would be useful to run on small portions of our data though?
 ====High Level Overview====
@@ Line 27: / Line 28: @@
-Build unsuccessfull:
+Build unsuccessful:
 ./ParallelVecUtilities.h: In function 'void ParallelSort(vec<T>&)':\\
@@ Line 39: / Line 40: @@
 ./ParallelVecUtilities.h: In function 'void ParallelWhatPermutation(const V&, vec<T3>&, C, bool)':\\
 ./ParallelVecUtilities.h:316: error: '__gnu_parallel' has not been declared
+Reading deeper into the documentation (the PDF attached to this page), I see that it requires gcc-4.3+. Campusrocks currently has gcc-4.1 installed. Perhaps if we compile the latest gcc we can install this program?
+Installed gcc-4.5! (had to do it myself, the sys admins wouldn't try)
+Note, if you compile with gcc-4.5 (or any of the other cc/c++-4.5) you will need to do one of the following:
+----------------------------------------------------------------------
+Libraries have been installed in:
+   /campusdata/BME235/lib/../lib64
+If you ever happen to want to link against installed libraries
+in a given directory, LIBDIR, you must either use libtool, and
+specify the full pathname of the library, or use the `-LLIBDIR'
+flag during linking and do at least one of the following:
+   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
+     during execution
+   - add LIBDIR to the `LD_RUN_PATH' environment variable
+     during linking
+   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
+   - have your system administrator add LIBDIR to `/etc/ld.so.conf'
+See any operating system documentation about shared libraries for
+more information, such as the ld(1) and ld.so(8) manual pages.
+----------------------------------------------------------------------
+While attempting to install Allpaths I get an error right away for all methods other than setting
+  LD_LIBRARY_PATH=/campusdata/BME235/lib:/campusdata/BME235/lib64
 ===== References =====
 <refnotes>notes-separator: none</refnotes>
 ~~REFNOTES cite~~

Banana Slug Genomics

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