Re: Problems about grab in Biopieces

[Martin Asser Hansen]

Hello Y-Ming

Biopieces only have rudimentary facilities to work with SAM/BAM format. For that you really need samtools. However, Biopieces will help you with a LOT of typical bioinformatic problems as illustrated in the Howto.

Now, it looks like the requirements for your Biopieces installation is missing different items. You should follow the installation instructions step by step. Send me the exact output of any error messages from the installation or from bp_test.

Cheers

Martin

On Fri, Mar 18, 2016 at 3:20 AM, Yu-Ming Hsu <ymhs...@gmail.com> wrote:

Hello, Maasha,

I am a research assistant in Taiwan Agricultural Research Institute, now focusing on developing molecular markers using NGS data. Lack of professional programming ability, I try to find some software which can help me to achieve my goal. Then I found "Biopieces", developed by you.

Now I tried to use grab to extract specific sequences from a fq file, and the name of each specific sequence is already collected in a txt file. But it turned out some problems. Both bp_test and my data showed some problem. Here I show you the result of my data.

yu-ming@yuming-VirtualBox:~/working_space$ read_fastq -i sample_AAGGG.fq | grab -E AAGGG_Aradu_spec_readname.txt
Error. You have specified 'C' as an Inline programming language.

I currently only know about the following languages:
    Foo, foo

If you have installed a support module for this language, try deleting the
config-x86_64-linux-5.022001 file from the following Inline DIRECTORY, and run again:

    /home/yu-ming/software/biopieces/tmp

(And if that works, please file a bug report.)

 at /home/yu-ming/software/biopieces/src/perl/Maasha/Common.pm line 47.
BEGIN failed--compilation aborted at /home/yu-ming/software/biopieces/src/perl/Maasha/Common.pm line 47.
Compilation failed in require at /home/yu-ming/software/biopieces/src/perl/Maasha/Match.pm line 35.
BEGIN failed--compilation aborted at /home/yu-ming/software/biopieces/src/perl/Maasha/Match.pm line 35.
Compilation failed in require at /home/yu-ming/software/biopieces/src/perl/Maasha/Biopieces.pm line 34.
BEGIN failed--compilation aborted at /home/yu-ming/software/biopieces/src/perl/Maasha/Biopieces.pm line 34.
Compilation failed in require at /home/yu-ming/software/biopieces/bin/grab line 32.
BEGIN failed--compilation aborted at /home/yu-ming/software/biopieces/bin/grab line 32.
/home/yu-ming/software/biopieces/src/ruby/lib/maasha/biopieces.rb:118:in `write': Broken pipe @ io_write - <STDOUT> (Errno::EPIPE)
    from /home/yu-ming/software/biopieces/src/ruby/lib/maasha/biopieces.rb:118:in `<<'
    from /home/yu-ming/software/biopieces/src/ruby/lib/maasha/biopieces.rb:118:in `puts'
    from /home/yu-ming/software/biopieces/bin/read_fastq:126:in `block (4 levels) in <main>'
    from /home/yu-ming/software/biopieces/src/ruby/lib/maasha/filesys.rb:104:in `each'
    from /home/yu-ming/software/biopieces/bin/read_fastq:108:in `block (3 levels) in <main>'
    from /home/yu-ming/software/biopieces/src/ruby/lib/maasha/filesys.rb:76:in `open'
    from /home/yu-ming/software/biopieces/bin/read_fastq:107:in `block (2 levels) in <main>'
    from /home/yu-ming/software/biopieces/bin/read_fastq:106:in `each'
    from /home/yu-ming/software/biopieces/bin/read_fastq:106:in `block in <main>'
    from /home/yu-ming/software/biopieces/src/ruby/lib/maasha/biopieces.rb:89:in `open'
    from /home/yu-ming/software/biopieces/bin/read_fastq:51:in `<main>'

I have read the instruction on the website, and there are several modules which I failed to download, including DBD::mysql, XML::Parser, SOAP::Lite and DB_File. Actually, my final goal is to get bam file with only specific sequences aligned on reference genome. That's why I am really interested in biopieces, which is such a useful software for me. Would you like to help me a little for this problem? Knowing you very busy, I will appreciate any response you give. Thanks a lot!

Sincerely,

Yu-Ming 

[Wannes Dermauw]

Hi

I encountered the same problem on my Max OSX. This problem was fixed after installing the following cpan modules:

sudo cpan install ExtUtils::MakeMaker

sudo cpan install Inline

sudo cpan install Inline::C

Regards

Wannes




Wannes

Op zaterdag 19 maart 2016 15:24:02 UTC+1 schreef maasha:

[Martin Asser Hansen]

Yes, there has been a change so that you need to install both Inline and Inline::C, before the one came with the other. The docs was updated accordingly.

Martin

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