hmmpgmd - daemon for database search web services

http://eddylab.org

HMMER 3.4                                           Aug 2023                                          hmmpgmd(1)

       Copyright (C) 2023 Howard Hughes Medical Institute.
       Freely distributed under the BSD open source license.

       For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source
       distribution, or see the HMMER web page (http://hmmer.org/).

       The  hmmpgmd  program  is the daemon that we use internally for the hmmer.org web server.  It essentially
       stands in front of the search programs phmmer, hmmsearch, and hmmscan.

       To use hmmpgmd, first an instance must be started up as a master server, and provided with at  least  one
       sequence  database  (using the --seqdb flag) and/or an HMM database (using the --hmmdb flag).  A sequence
       database must be in hmmpgmd format, which may be produced using esl-reformat.  An HMM database is of  the
       form  produced  by  hmmbuild.   The  input database(s) will be loaded into memory by the master. When the
       master has finished loading the database(s), it prints the line: "Data  loaded  into  memory.  Master  is
       ready."

       After  the master is ready, one or more instances of hmmpgmd may be started as workers. These workers may
       be (and typically are) on different machines from the master, but must have access to the  same  database
       file(s) provided to the master, with the same path. As with the master, each worker loads the database(s)
       into memory, and indicates completion by printing: "Data loaded into memory. Worker is ready."

       The  master  process and workers are expected to remain running.  One or more clients then connect to the
       master and submit possibly many queries. The master distributes the work of a query  among  the  workers,
       collects  results,  and  merges  them  before  responding  to the client. Two example client programs are
       included in the HMMER src directory - the C program hmmc2 and the perl script  hmmpgmd_client_example.pl.
       These are intended as examples only, and should be extended as necessary to meet your needs.

       A  query  is  submitted to the master from the client as a character string. Queries may be the sort that
       would normally be handled by phmmer (protein sequence vs protein database), hmmsearch (protein HMM  query
       vs protein database), or hmmscan (protein query vs protein HMM database).

       The  general  form  of  a client query is to start with a single line of the form @[options], followed by
       multiple lines of text representing either the query HMM or fasta-formatted sequence. The final  line  of
       each query is the separator //.

       For  example,  to  perform a phmmer type search of a sequence against a sequence database file, the first
       line is of the form @--seqdb1, then the fasta-formatted query sequence starting  with  the  header  line
       >sequence-name, followed by one or more lines of sequence, and finally the closing //.

       To  perform  an  hmmsearch type search, the query sequence is replaced by the full text of a HMMER-format
       query HMM.

       To perform an hmmscan type search, the text matches that of the phmmer type search, except that the first
       line changes to @--hmmdb1.

       In the hmmpgmd-formatted sequence database file, each sequence can be associated with one  or  more  sub-
       databases.  The  --seqdb  flag  indicates which of these sub-databases will be queried.  The HMM database
       format does not support sub-databases.

       hmmpgmd - daemon for database search web services

-h     Help; print a brief reminder of command line usage and all available options.

       --master
              Run as the master server.

       --worker<s>
              Run as a worker, connecting to the master server that is running on IP address <s>.

       --cport<n>
              Port to use for communication between clients and the master server.  The default is 51371.

       --wport<n>
              Port to use for communication between workers and the master server.  The default is 51372.

       --ccncts<n>
              Maximum number of client connections to accept. The default is 16.

       --wcncts<n>
              Maximum number of worker connections to accept. The default is 32.

       --pid<f>
              Name of file into which the process id will be written.

       --seqdb<f>
              Name of the file (in hmmpgmd format) containing protein sequences.  The contents of this file will
              be cached for searches.

       --hmmdb<f>
              Name of the file containing protein HMMs. The contents of this file will be cached for searches.

       --cpu<n>
              Number of parallel threads to use (for --worker ).

       See hmmer(1) for a master man page with a list of all the individual man pages for programs in the  HMMER
       package.

       For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or
       see the HMMER web page (http://hmmer.org/).

hmmpgmd [options]