Installing CASAVA on OS X 10.6.5 Snow Leopard

[trevor]

I attempted to install Casava on OS X (10.6.5 Snow Leopard) and it didn't go so well out of the box. I was told it's not supported. I did a cursory search for others that have done this and didn't see anything.

These were the steps I took to get an executable CASAVA binary installed - it seems like it wouldn't be that hard to be rolled into the official installation.

I'm using GCC 4.5.1 (installed with MacPorts and managed with gcc_select), but this will likely work with the standard GCC 4.2.1 installation.

Here's my setup:

  % sw_vers
  ProductName:    Mac OS X
  ProductVersion: 10.6.5
  BuildVersion:   10H574

  % gcc --version
  gcc (GCC) 4.5.1

- Step 1
-- Update CMake to at least 2.8.3

CMake needs to be updated to work with the latest version of OS X, or else you'll get "jni.h" not found errors.

It's available here -

http://www.cmake.org/cmake/resources/software.html

Check where it gets installed, likely /usr/local/bin

  % which cmake
  /usr/local/bin/cmake
  % cmake --version
  cmake version 2.8.3

- Step 2
-- Get ChartDirector for Perl on OS X

  cd /tmp
  curl -O http://download2.advsofteng.com/chartdir_perl_mac.tar.gz
  tar xvf chartdir_perl_mac.tar.gz

- Step 3
-- Expand CASAVA

  tar xvf CASAVA_v1.7.0.tar.bz2
  cd CASAVA_v1.7.0
  mkdir CASAVA-build

- Step 4
-- Emend packaged CodeMin

  cd redist
  tar xvf CodeMin-1.0.1.tar.gz
  mv CodeMin-1.0.1.tar.gz CodeMin-1.0.1.tar.gz.orig

Now edit CodeMin-1.0.1/include/test_float.h -

line 64 is -
is_float_nan(FloatType x){ return isnan(x); }

change line 64 to -
is_float_nan(FloatType x){ return std::isnan(x); }


line 68 is -
is_float_inf(FloatType x){ return isinf(x); }

change line 68 to -
is_float_inf(FloatType x){ return std::isinf(x); }


And then recreate the package -

  tar cvf CodeMin-1.0.1.tar.gz CodeMin-1.0.1
  cd ..

- Step 5
-- Update src files

A few modifications to the files in the 'src' directory. Here's the patchfile.

diff --git c++/include/alignment/GlobalUtilities.hh c++/include/alignment/GlobalUtilities.hh
index 2aec781..77eccce 100644
--- c++/include/alignment/GlobalUtilities.hh
+++ c++/include/alignment/GlobalUtilities.hh
@@ -37,6 +37,10 @@ AUTHOR: A. J. Cox
 // inner_product requires numeric
 #include <numeric>
 
+typedef unsigned int uint;
+typedef unsigned char uchar;
+typedef unsigned short ushort;
+#include <iostream>
 #include "common/Sequence.hh"
 
 // Identifier to embed in source and binary files
@@ -47,9 +51,6 @@ AUTHOR: A. J. Cox
 using namespace std;
 namespace fs = boost::filesystem;
 
-typedef unsigned int uint;
-typedef unsigned char uchar;
-typedef unsigned short ushort;
 
 static const char baseNames [] = "ACGT";
 
diff --git c++/include/alignment/aligner.h c++/include/alignment/aligner.h
index d52e45b..d8fce73 100755
--- c++/include/alignment/aligner.h
+++ c++/include/alignment/aligner.h
@@ -35,6 +35,7 @@
 
 using namespace std;
 
+typedef unsigned int uint;
 typedef unsigned char uchar;
 
 #define QUALSCALE 0.0333
diff --git c++/include/common/Alignment.hh c++/include/common/Alignment.hh
index 9df4c45..503e45a 100644
--- c++/include/common/Alignment.hh
+++ c++/include/common/Alignment.hh
@@ -19,6 +19,7 @@
 #ifndef CASAVA_COMMON_ALIGNMENT_HH
 #define CASAVA_COMMON_ALIGNMENT_HH
 
+#include "alignment/GlobalUtilities.hh"
 #include "common/Sequence.hh"
 
 namespace casava
diff --git c++/include/common/Sequence.hh c++/include/common/Sequence.hh
index b0490dd..46fc61d 100644
--- c++/include/common/Sequence.hh
+++ c++/include/common/Sequence.hh
@@ -26,6 +26,9 @@
 #include <string>
 #include <vector>
 
+typedef unsigned int uint;
+typedef unsigned char uchar;
+typedef unsigned short ushort;
 #include "common/Spot.hh"
 #include "common/FilteringStreams.hh"
 
diff --git c++/lib/alignment/aligner.cpp c++/lib/alignment/aligner.cpp
index f3c87c2..43b7a2d 100755
--- c++/lib/alignment/aligner.cpp
+++ c++/lib/alignment/aligner.cpp
@@ -26,6 +26,7 @@
 
 using namespace std;
 
+typedef unsigned int uint;
 typedef unsigned char uchar;
 
 #define QUALSCALE 0.0333
diff --git c++/lib/applications/AlignCandIndelReads.cpp c++/lib/applications/AlignCandIndelReads.cpp
index 0795f21..b78a80b 100644
--- c++/lib/applications/AlignCandIndelReads.cpp
+++ c++/lib/applications/AlignCandIndelReads.cpp
@@ -122,7 +122,7 @@ int AlignCandIndelReads::run()
     if (line[0] == '#') { continue; }
 
     // Load export line into export record object
-    Export::Export record(line, 1);
+    Export record(line, 1);
 
     // Get reference region to align tag too
     string refSeq;

- Step 6
-- Configure and compile

Goto the CASAVA-build directory.

  ../src/configure --with-cmake=/usr/local/bin/cmake
  make
  make install

'make install' will crash with a CMake permissions error. This is where you want to update ChartDirector.



- Step 7
-- Update ChartDiretor

In the current CASAVA-build directory -

  mkdir -p opt/ChartDirector/Darwin/i386/lib/fonts
  touch opt/ChartDirector/Darwin/i386/lib/chartdir.lic
  cp -R /tmp/ChartDirector/lib/* opt/ChartDirector/Darwin/i386/lib/fonts

- Step 8
-- Final install

In the current CASAVA-build directory -

  sudo make install

You should now have CASAVA installed.

  % /usr/local/bin/CASAVA --version
  Info: @CASAVA_VERSION_FULL@

[husamia]

I heard 1.8 if not already available, have you tried it?

[trevor]

I heard 1.8 if not already available, have you tried it?

Yesterday Illumina Technical Support told me only 1.7.0 is available. Could you clarify?

From their email on 2010-11-30:
"CASAVA 1.7.0 is the latest version available. Unfortunately we do not support or test it on OS X."

[husamia]

I was talking to a core facility about data transfer and they mentioned this to me. I can't confirm it. Its probably not true or proposed update and I don't know when.

[drio]

Not to discorage you, but I'd suggest you install some virtualization software and install a linux vm. You will have some performance penalty but the installation will be trivial.

[KiTrinet]

Please excuse my naivety as I am not as proficient as you guys. I wanted to know the patch file that you suggested to install. Do i need to create a new patchfile or should i include in some other file. If I have to create a new patch file how do I have to name it and should i just save it in ~/Casava_v1.8.2/scr or elsewhere. Thanks in advance for any suggestions

[trevor]

Hi KiTrinet,

This thread is from the past.

What are you attempting to do?

[KiTrinet]

Hi Trevor,

Many thanks for your prompt reply. I am trying to install casava on my mac so i can convert the txt files to fastq format. I have followed your thread step by step however I am not properly understanding when you talk about "A few modifications to the files in the 'src' directory. Here's the patchfile." Do I have to create a patchfile or do I just copy that into a source file (if this is the case where should I copy it)

With Kind Regards,

Kreshnik

[trevor]

This thread was in reference to CASAVA version 1.7.0, the latest version right now is 1.8.2, which it appears you have. These instructions are likely out of date.