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--- archive:bioinformatic_tools:allpaths [2010/04/07 08:37]
jstjohn
+++ archive:bioinformatic_tools:allpaths [2010/04/19 06:21]
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 25: / Line 26: @@
   Boost successfully installed. Now installing allpaths. Configure successful and currently building. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/07 00:53//
+Build unsuccessful:
+./ParallelVecUtilities.h: In function 'void ParallelSort(vec<T>&)':\\
+./ParallelVecUtilities.h:27: error: '__gnu_parallel' has not been declared\\
+./ParallelVecUtilities.h: In function 'void ParallelSort(vec<T>&, StrictWeakOrdering)':\\
+./ParallelVecUtilities.h:35: error: '__gnu_parallel' has not been declared\\
+./ParallelVecUtilities.h: In function 'void ParallelReverseSort(vec<T>&)':\\
+./ParallelVecUtilities.h:42: error: '__gnu_parallel' has not been declared\\
+./ParallelVecUtilities.h: In function 'void ParallelReverseSort(vec<T>&, StrictWeakOrdering)':\\
+./ParallelVecUtilities.h:50: error: '__gnu_parallel' has not been declared\\
+./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)
+The gcc/g++-4.5 libraries are installed in:
+  /campusdata/BME235/lib
+  /campusdata/BME235/lib64
+To compile with the gcc 4.5 compilers you need to have your environment properly set up so that everything knows where to look for the linked libraries. I did this by setting my LD_LIBRARY_PATH variable as follows in my .profile
+  LD_LIBRARY_PATH=/campusdata/BME235/lib:/campusdata/BME235/lib64:$LD_LIBRARY_PATH
+  export LD_LIBRARY_PATH
+Note if you want to run the install via a script, an example script that sets up environmental variables is here:
+  /campusdata/BME235/programs/allpaths/allpaths3-3.2/installallpaths.sh
+I have encountered a new error much further along in the compilation.  To view the error see the last 40 lines of file:
+  /campus/BME235/programs/allpaths/allpaths3-3.2/installallpaths.sh.o2730
+  /campusdata/BME235/programs/allpaths/allpaths3-3.2/src/paths/MuxWalkGraph.cc:740: undefined reference to `digraphE<KmerPath>::TransferEdges(int, int, unsigned char)'
 ===== References =====
 <refnotes>notes-separator: none</refnotes>
 ~~REFNOTES cite~~

Banana Slug Genomics

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