Hi all! Here are the instructions to install Bioperl under Cygwin. Following it are instructions for MacOSX or Unix, scroll to the end. In case of problems, please mail me at rarnold@kimlab.org ! Pre-requisit: find a fast Internet connection and take some time off from other duties. This will last ~30-60 min. but it is worth it, Bioperl can solve many problems for you in the future! I propose to get a cup of coffee/tee before.... To install Bioperl in Cygwin, following steps must be done: Achtung (Attention)! For Windows XP, following step must be done:
for all windows versions, proceed as follows: 1. we need following packages installed in Cygwin: perl, make, binutils, and gcc we install missing ones by re-running the setup.exe of Cygwin: (if you cannot find it anymoer, simply download Cygwin again from the internet) use search function in the package selection dialog chose by clicking in the column 'New' and activating the 'Bin' checkboxes perl: Larry Pages .... make: the GNU version of the 'make' utility binutils: binutils, the GNU assembler, linker and binary utilities gcc: gcc-core go to next... 2. open a cygwin terminal type perl -MCPAN -e shell then type o conf prerequisites_policy follow o conf commit install Bundle::CPAN this installs the installation utility for further Perl add ons (called modules, as Bioperl) if the installation is finsihed (nothing happens in the console), do following command install Module::Build Step 2) now, we install the actual version of bioperl type: d /bioperl/ and you will get a list of different versions. We use this one: 'CJFIELDS/BioPerl-1.6.1.tar.gz' and install it by install CJFIELDS/BioPerl-1.6.1.tar.gz if you encounter problems, with the firewall, allow FTP access if the process asks Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] answer with 'n' (Answer means type n and then hit the return button) if it asks Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a] answer with 'a' then it will ask Do you want to run tests that require connection to servers across the internet answer with 'n' if the process wants a decision like 'install [a]ll optional external modules, press return (this is selection 'n') no it takes a while. Don't be confused if error messages appear in the first place or the program seems to do nothing for a while.... The process is finished Writing /usr/lib/perl5/site_perl/5.10/i686-cygwin/auto/Bio/.packlist Will try to install symlinks to /usr/local/bin CJFIELDS/BioPerl-1.6.1.tar.gz ./Build install -- OK if so, proceed: type q to quit the perl update program You might now create a test perl program like this: #!/usr/bin/perl use Bio::DB::Fasta; use strict; my $file=$ARGV[0]; my $id=$ARGV[1]; my $db = Bio::DB::Fasta->new($file); # one file or many files my $seqstring = $db->seq($id); # get a sequence as string my $seqobj = $db->get_Seq_by_id($id); # get a PrimarySeq obj my $desc = $db->header($id); # get the header, or description line print $seqstring; this reads a multi-fasta file given as first command line argument and returns the sequence of the entry given as second argument Instructions for installing BioPerl 1.6.1 for MacOSX or Unix: Open a shell and type gcc. If you get an error then you must install XCode from here. Download BioPerl 1.6.1 from here . Then follow the instructions below. This is an interactive installation so if at some point, the installation prompts to download something from CPAN respond with yes. It takes a while and there will be alot of output. INSTALLING BIOPERL THE EASY WAY USING Build.PL The advantage of this approach is it's stepwise, so it's easy to stop and analyze in case of any problem. Download, then unpack the tar file. For example: >tar xvfz BioPerl-1.6.1.tar.gz >cd BioPerl-1.6.1 Now issue the build commands: >sudo perl Build.PL >./Build test If you've installed everything perfectly and all the network connections are working then you may pass all the tests run in the './Build test' phase. It's also possible that you may fail some tests. Possible explanations: problems with local Perl installation, network problems, previously undetected bug in BioPerl, flawed test script, problems with CGI script using for sequence retrieval at public database, and so on. Remember that there are over 900 modules in BioPerl and the test suite is running more than 12000 individual tests, a few failed tests may not affect your usage of BioPerl. If you decide that the failed tests will not affect how you intend to use BioPerl and you'd like to install anyway, or if all tests were fine, do: >sudo ./Build install This is what most experienced BioPerl users would do. However, if you're concerned about a failed test and need assistance or advice then contact bioperl-l@bioperl.org. (You could provide us the detailed results of the failed test(s): see the `THE TEST SYSTEM' below for information on how to generate such results.) To './Build install' you need write permission in the perl5/site_perl/source area (or similar, depending on your environment). Usually this will require you becoming root, so you will want to talk to your systems manager if you don't have the necessary privileges. It is also straightforward to install the package outside of the this standard Perl5 location. See INSTALLING BIOPERL IN A PERSONAL MODULE AREA, below. You might now create a test perl program like this: #!/usr/bin/perl use Bio::DB::Fasta; use strict; my $file=$ARGV[0]; my $id=$ARGV[1]; my $db = Bio::DB::Fasta->new($file); # one file or many files my $seqstring = $db->seq($id); # get a sequence as string my $seqobj = $db->get_Seq_by_id($id); # get a PrimarySeq obj my $desc = $db->header($id); # get the header, or description line print $seqstring; this reads a multi-fasta file given as first command line argument and returns the sequence of the entry given as second argument. Try downloading a proteome from Ensembl like Homo_sapiens.GRCh37.56.pep.all.fa and query for a sequence using it's Ensembl id like this: perl test.pl Homo_sapiens.GRCh37.56.pep.all.fa ENSP00000375979
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