[maker-devel] install maker on cluster
Christoph Hahn
chrisi.hahni at gmail.com
Tue Oct 16 08:02:36 MDT 2012
Thanks for your help Carson!
I tried maker2.26, but the error still remains. I also tried to change
the TMP= option in the maker_opts file, but no change either..
STATUS: Parsing control files...
ERROR: The HMM file[s] provided for gmhmm do not exist:
When building the maker2.26 I saw that it is complaining about one more
(recommended) dependency (I must have overlooked that before):
Checking prerequisites...
recommends:
* DBD::Pg is not installed
I am having problems to get that one.. Is that causing the error?
much obliged,
Christoph
Am 15.10.2012 20:05, schrieb Carson Holt:
> It looks like either an NFS issue or perhaps an issue with the location
> provided for the TMP= in the maker_opts.ctl file.
>
> First I would suggest trying maker 2.26 to see if the issue still happens
> there (there are a few updates to how NFS locks are handled in 2.26).
>
> Second if you are setting TMP make sure your disk is not full. Or if TMP
> was set to a tmpfs location (in memory filesystem), it could be a full
> memory issue in which case you could just set TMP to somewhere else.
>
> Let me know if you still see the issue in 2.26 or after changing the
> location of TMP.
>
> Thanks,
> Carson
>
>
> On 12-10-12 1:09 PM, "Christoph Hahn" <chrisi.hahni at gmail.com> wrote:
>
>> Hi Carson,
>>
>> Thanks for your reply. I managed to install maker2.25 properly now, but
>> when running it I am getting strange errors (two kinds):
>> type one:
>> STATUS: Parsing control files...
>> ERROR: The HMM file[s] provided for gmhmm do not exist:
>>
>> type two:
>> STATUS: Parsing control files...
>> ERROR: Cannot get initialization lock.
>>
>> I have divided the draft assembly to several files, each containing a
>> subset of contigs on which I am running a maker instance. I am getting
>> the above named error type one for the majority of the instances,
>> although the HMM file it is complaining about (es.mod) is actually in
>> the path it is naming (not shown above). In a small number of instances
>> I am getting the type two error mentioned above.
>>
>> Can you help me?
>>
>> much obliged,
>> Christoph
>>
>>
>>
>> On 09.10.2012 18:27, Carson Holt wrote:
>>> You may need to reconfigure your cpan preferences.
>>>
>>> You can do this manually by editing the ~/.cpan/CPAN/MyConfig.pm file,
>>> or
>>> by starting cpan from your command line (command is cpan). Then run 'o
>>> conf init' inside the cpan ui.
>>>
>>> --Carson
>>>
>>>
>>> On 12-10-09 7:07 AM, "Christoph Hahn"<chrisi.hahni at gmail.com> wrote:
>>>
>>>> Hello maker-team,
>>>>
>>>> I am trying to install maker 2.25 on a cluster, without root privileges
>>>> (I managed before, but now after migration to a new cluster I cant seem
>>>> to get it to work). All necessary prerequisite programs are installed
>>>> and in the path (I followed the steps in the INSTALL file that comes
>>>> with maker2.25). When I do: perl Build.PL, I get:
>>>> Checking prerequisites...
>>>> requires:
>>>> ! DBD::SQLite is not installed
>>>> ! IO::All is not installed
>>>> ! Inline::C is not installed
>>>> ! Perl::Unsafe::Signals is not installed
>>>> ! Proc::ProcessTable is not installed
>>>> ! Want is not installed
>>>> ! forks is not installed
>>>> ! forks::shared is not installed
>>>> build_requires:
>>>> ! LWP::Simple is not installed
>>>> recommends:
>>>> * DBD::Pg is not installed
>>>>
>>>> ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the
>>>> versions
>>>> of the modules indicated above before proceeding with this installation
>>>>
>>>> Run 'Build installdeps' to install missing prerequisites.
>>>>
>>>> MAKER supports distributed parallelization via MPI.
>>>> Would you like to configure MAKER for MPI (This
>>>> requires that you have an MPI client installed)? [N ]n
>>>>
>>>> WARNING: Apache cannot be located. The optional web based
>>>> interface to MAKER will not be available to you.
>>>>
>>>> Created MYMETA.yml and MYMETA.json
>>>> Creating new 'Build' script for 'MAKER' version '2.25'
>>>>
>>>>
>>>> The file 'Build' has been created for you to finish installing MAKER.
>>>>
>>>>
>>>>
>>>> ========================================================================
>>>> ==
>>>> ====
>>>> STATUS MAKER 2.25
>>>>
>>>> ========================================================================
>>>> ==
>>>> ====
>>>> PERL Dependencies: MISSING
>>>> ! forks
>>>> ! IO::All
>>>> ! forks::shared
>>>> ! Want
>>>> ! DBD::SQLite
>>>> ! Proc::ProcessTable
>>>> ! Inline::C
>>>> ! Perl::Unsafe::Signals
>>>>
>>>> External Programs: VERIFIED
>>>> External C Libraries: VERIFIED
>>>> MPI SUPPORT: DISABLED
>>>> MWAS Web Interface: DISABLED
>>>> MAKER PACKAGE: MISSING PREREQUISITES
>>>>
>>>>
>>>> Important Commands:
>>>> ./Build installdeps #installs missing PERL dependencies
>>>> ./Build installexes #installs all missing external
>>>> programs
>>>> ./Build install #installs MAKER
>>>> ./Build status #Shows this status menu
>>>>
>>>> Other Commands:
>>>> ./Build repeatmasker #installs RepeatMasker (asks for
>>>> RepBase)
>>>> ./Build blast #installs BLAST (NCBI BLAST+)
>>>> ./Build exonerate #installs Exonerate (v2 on UNIX / v1
>>>> on
>>>> Mac OSX)
>>>> ./Build snap #installs SNAP
>>>> ./Build augustus #installs Augustus
>>>> ./Build apollo #installs Apollo
>>>> ./Build gbrowse #installs GBrowse (must be root)
>>>> ./Build jbrowse #installs JBrowse (MAKER copy, not web
>>>> accecible)
>>>> ./Build mpich2 #installs MPICH2 (but manual install
>>>> recommended)
>>>>
>>>> So it seems some Perl Dependencies are missing. As indicated in INSTALL
>>>> I followed the quick and dirty installation for Bioperl, so I am not
>>>> sure what I did wrong/missed out.
>>>>
>>>> When I run ./Build installdeps, I get:
>>>> You do not have write access to install missing Modules.
>>>> I can try and install these locally (i.e. only for MAKER)
>>>> in the .../maker/perl/lib directory, or you can run
>>>> './Build installdeps' as root or using sudo and try again.
>>>> Do want MAKER to try and build a local installation? [N ]y
>>>> mkdir /usit/titan: Permission denied at
>>>> /cluster/software/VERSIONS/perlmodules-5.10_1/lib/perl5/CPAN/FTP.pm
>>>> line
>>>> 59
>>>>
>>>> Sorry to bother you with this minor things!! Any help would me much
>>>> appreciated!
>>>>
>>>> much obliged,
>>>> Christoph
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>
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