I did so, but I started getting different errors which apaprently come from the different in the samtools and Bio::DB::Sam versions. I had downloaded the newest version of samtools which apparently the Bio::DB::Sam doesn't supoprt anymore. There were some functions which were commented out in the new samtools bam.h library. I am gonig to download and install an older version of samtools and try to link Bio::DB::Sam to the old version of samtools and will keep here posted on the results.–Aug 29 '14 at 18:13.
Here is a script that will fetch the SAMtools source and compile it, then fetch and compile the Perl bindings. Wget xjf samtools-0.1.18.tar.bz2 && cd samtools-0.1.18make CFLAGS=-fPICexport SAMTOOLS=`pwd`cpanm Bio::DB::SamPart of the problem you were likely seeing is that the SAMtools project has recently undergone some major code reorganization (and this has naturally made it difficult to work with external language bindings). I followed instructions from README file below of Bio-SamTools-1.43 to edit the Makefile in samtools 0.1.17. Then, to install, I usedperl -MCPAN -e shellinstall Bio::DB::SamREADME:This is a Perl interface to the SAMtools sequence alignmentinterface. It ONLY works on versions of Samtools up to 0.1.17.
Build GSNAP Databases and BWA Indexes that can be re-used for aligning to whole genomes. View and save quality scores and metadata of your NGS raw data files with FastQC reports. Generate Variant Calling Files (VCF) to flag variants in your NGS alignments using SAMtools. RNA-Seq: Expanded Cufflinks suite with the addition of Cuffquant and Cuffnorm.
It doesnot work on version 1.0 or higher due to major changes in the librarystructure.See for samtools documentation. ONE-STEP INSTALLATIONIn the root directory of this distribution you will find the scriptINSTALL.pl. Running this will download the latest versions of thismodule and SamTools into a temporary directory, compile them, test andinstall. Simply run:perl INSTALL.pl. MULTI-STEP INSTALLATIONThe more traditional install requires you to separately download,unpack and compile SAMtools 0.1.10 through 0.1.17 in some accessibledirectory.
Typing 'make' in the samtools directory will usuallywork. SAMtools versions 0.1.18 and higher do not work with thislibrary.Then set the environment variable SAMTOOLS to point to this directory.You will also need to install Bio::Perl from CPAN.Now run:perl Build.PL./Build./Build test(sudo)./Build installTROUBLESHOOTING:If you encounter problems during compiling, you may need to editBuild.PL so that extracompilerflags matches the CFLAGS and DFLAGSsettings in the Samtools Makefile. Here are some common problems:.
When building this module, you get an error like the following:relocation RX866432 against `a local symbol' can not be used whenmaking a shared object; recompile with -fPICTo fix this, edit the Makefile in the Samtools distribution by adding'-fPIC' to the CFLAGS line. While you're at it, you may also wish toget rid of a bunch of unused variable warnings that appears underrecent versions of gcc. The modified CFLAGS will look like thisCFLAGS= -g -Wall -Wno-unused -Wno-unused-result -O2 -fPIC #-m64 #-arch ppcThen do 'make clean; make' in the Samtools directory to recompile thelibrary. After this you should be able to build this module withouterrors. When building this module, you get an error about a missing mathlibrary.To fix this, follow the recipe in (1) except add -m64 to CFLAGS so itlooks like this:CFLAGS= -g -Wall -O2 -fPIC #-m64 #-arch ppcTESTING AND CONTRIBUTING:You can obtain the most recent development version of this module viaits GitHub site at. Pleasefeel free to submit bug reports, patches, etc.
Via GitHub.AUTHOR:Lincoln D. SteinCopyright (c) 2009-2015 Ontario Institute for Cancer ResearchThis package and its accompanying libraries are free software; you canredistribute it and/or modify it under the terms of the ArtisticLicense 2.0, the Apache 2.0 License, or the GNU General Public License(version 1 or higher). Refer to LICENSE for the full license text.
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