Anybody interested in running OLB/Casava on Solaris?

[dawe]

Hi all,
If there's anybody interested in installing the Illumina pipeline on recent OpenSolaris (actually I've done this on Nexenta CP3) release to take advantage of ZFS dedup and compression, I've got a couple of patches that may be useful to allow for a proper build... The OLB works fine for me, still waiting for the results of the alignment step :-)

d

[Mercutio]

Hi,
I'm curently trying to make casava work onsolaris.
If you have some advices...

Thanks

Jeremy

[dawe]

Hi,
I'm curently trying to make casava work onsolaris.
If you have some advices...

Thanks

Jeremy

What error do you exactly get? I had to apply these patches

diff -Naur CASAVA_v1.6.0/c++/blt_util/stream_stat.cpp /opt/Illumina/CASAVA_v1.6.0/c++/blt_util/stream_stat.cpp
--- CASAVA_v1.6.0/c++/blt_util/stream_stat.cpp  2009-10-06 17:50:28.000000000 +0200
+++ /opt/Illumina/CASAVA_v1.6.0/c++/blt_util/stream_stat.cpp    2010-05-07 10:08:10.579282690 +0200
@@ -20,7 +20,7 @@
 operator<<(std::ostream& os,const stream_stat& ss) {
 
     os << "sample_size: " << ss.sample_size() << " min: " << ss.min() << " max: " << ss.max()
-       << " mean: " << ss.mean() << " sd: " << ss.sd() << " se: " << ss.stderr();
+       << " mean: " << ss.mean() << " sd: " << ss.sd() << " se: " << ss.std_err();
 
     return os;
 }
diff -Naur CASAVA_v1.6.0/c++/blt_util/stream_stat.hh /opt/Illumina/CASAVA_v1.6.0/c++/blt_util/stream_stat.hh
--- CASAVA_v1.6.0/c++/blt_util/stream_stat.hh   2009-10-06 17:50:28.000000000 +0200
+++ /opt/Illumina/CASAVA_v1.6.0/c++/blt_util/stream_stat.hh     2010-05-07 10:08:01.594626290 +0200
@@ -46,7 +46,7 @@
     double mean() const { return ((k_<1) ? nan() : M_); }
     double variance() const { return ((k_<2) ? nan() : Q_/(static_cast<double>(k_-1))); }
     double sd() const { return std::sqrt(variance()); }
-    double stderr() const { return sd()/std::sqrt(static_cast<double>(k_)); }
+    double std_err() const { return sd()/std::sqrt(static_cast<double>(k_)); }
 
 private:
     static

and

diff -Naur CASAVA_v1.6.0/opt/CodeMin/include/test_float.h /opt/Illumina/CASAVA_v1.6.0/opt/CodeMin/include/test_float.h
--- CASAVA_v1.6.0/opt/CodeMin/include/test_float.h      2009-03-16 21:30:30.000000000 +0100
+++ /opt/Illumina/CASAVA_v1.6.0/opt/CodeMin/include/test_float.h        2010-05-07 10:15:35.012567234 +0200
@@ -34,9 +34,9 @@
 #ifndef __TEST_FLOAT_H
 #define __TEST_FLOAT_H
 
-#ifndef DARWIN_HACK
+//#ifndef DARWIN_HACK
 #include <cmath>
-#endif
+//#endif
 
 namespace codemin {
 
@@ -46,7 +46,7 @@
 
 
 // replacements for BSD libc's
-#ifdef DARWIN_HACK
+//#ifdef DARWIN_HACK
 
 template <typename FloatType>
 bool
@@ -56,6 +56,7 @@
 bool
 is_float_inf(FloatType x){ return is_float_nan(x*0) && (! is_float_nan(x)); }
 
+/*
 #else
 
 
@@ -68,7 +69,7 @@
 is_float_inf(FloatType x){ return isinf(x); }
 
 #endif
-
+*/
 
 template <typename FloatType>
 bool
@@ -78,5 +79,5 @@
 
 }
 
-#endif
 
+#endif

$ uname -a
SunOS host001.instruments 5.11 NexentaOS_134f i86pc i386 i86pc Solaris

$ gcc -v
Using built-in specs.
Target: i386-pc-solaris2.11
Configured with: ../src/configure -v --enable-languages=c,c++,fortran,objc,obj-c++,treelang --prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.2 --program-suffix=-4.2 --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --enable-mpfr --disable-libmudflap --enable-targets=all --disable-libssp --enable-checking=release --build=i386-pc-solaris2.11 --host=i386-pc-solaris2.11 --target=i386-pc-solaris2.11 --with-gnu-ld --with-gnu-as --with-ld=/usr/bin/ld --with-as=/usr/bin/as
Thread model: posix
gcc version 4.2.3 (Ubuntu 4.2.3-2nexenta7)

I know I'm using nexenta, but basically it should work on solaris too...

HTH

d

[Mercutio]

Hi,

Thanks for your reply.
For the stream_stat.hh and .cpp, i've done the same solution.

In the test_float.h i've define DARWINHACK (because i made it run on MacOs too).

I have to add #include <cstdlib> in contig_info.cpp

and remove the remove -D_USE_KNETFILE from samtools Makefile.

Now, I've just to get the ChartDirector file for SunOS and i hope it will work

So for me, it was a little bit more complicated...

Thanks for your help

Jeremy

[cabroadb]

Jeremy,

Did you get OLB to compile on MacOS as well as CASAVA?

Carl

[dawe]

Jeremy,

Did you get OLB to compile on MacOS as well as CASAVA?

Carl

Hi, I have successfully tried once, I may try with recent version if you want...

d

[Mercutio]

I can try also.
I may have time today.

Jeremy

[cabroadb]

I started a new thread for the MacOS building comments.

http://seqanswers.com/forums/showthread.php?p=22854

[sweet_dna_girl]

hi, does anyone know if the illumina OLB source code is online somewhere? I'd like to look at it. thanks!!

[sklages]

hi, does anyone know if the illumina OLB source code is online somewhere? I'd like to look at it. thanks!!

You can download it from their web site if you have an iCom account ..

[sweet_dna_girl]

oh ok, thanks! so it's the source code, and not the binaries? do you know where on the website to look once you log in?

[sklages]

oh ok, thanks! so it's the source code, and not the binaries? do you know where on the website to look once you log in?

Yes, the sources. Including boost and seqan. Have a look somewhere under "Download/Listing/Software" ..

cheers, Sven

[sweet_dna_girl]

thanks! Does this include the bustard.py basecaller? Do you know if I can find bustard on the open internet?

[sklages]

thanks! Does this include the bustard.py basecaller? Do you know if I can find bustard on the open internet?

Yes, it does include bustard.py and no, you won't find bustard in the "open internet".