[maker-devel] install maker on cluster

Carson Holt carsonhh at gmail.com
Tue Oct 16 08:19:21 MDT 2012 

No. that's just a recommendation for the maker2chado script to work.

Is es.mod the actual HMM or a soft link to the HMM?
After the error message their should be a list of the actual files.  Does
it print that?
Are there trailing commas in you maker_opts.ctl file after the hmm file
name in the control files?
Are their ':' characters in the path name to the file?

--Carson



On 12-10-16 10:02 AM, "Christoph Hahn" <chrisi.hahni at gmail.com> wrote:

>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.or
>>>>>g
>>>>
>>
>
>

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