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<h1 id="NAME">NAME</h1>

<pre><code>    init_pipeline.pl</code></pre>

<h1 id="SYNOPSIS">SYNOPSIS</h1>

<pre><code>    init_pipeline.pl &lt;config_module_or_filename&gt; [-help | [-analysis_topup | -job_topup] &lt;options_for_this_particular_pipeline&gt;]</code></pre>

<h1 id="DESCRIPTION">DESCRIPTION</h1>

<pre><code>    init_pipeline.pl is a generic script that is used to create+setup=initialize eHive pipelines from PipeConfig configuration modules.</code></pre>

<h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>

<pre><code>        # get this help message:
    init_pipeline.pl

        # initialize a generic eHive pipeline:
    init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf -password &lt;yourpassword&gt;

        # see what command line options are available when initializing long multiplication example pipeline
        #   (assuming your current directory is ensembl-hive/modules/Bio/EnsEMBL/Hive) :
    init_pipeline.pl PipeConfig/LongMult_conf -help

        # initialize the long multiplicaton pipeline by supplying not only mandatory but also optional data:
        #   (assuming your current directory is ensembl-hive/modules/Bio/EnsEMBL/Hive/PipeConfig) :
    init_pipeline.pl LongMult_conf -password &lt;yourpassword&gt; -first_mult 375857335 -second_mult 1111333355556666 </code></pre>

<h1 id="OPTIONS">OPTIONS</h1>

<pre><code>    -help            :   Gets this help message and exits

    -analysis_topup  :   A special initialization mode when (1) pipeline_create_commands are switched off and (2) only newly defined analyses are added to the database
                         This mode is only useful in the process of putting together a new pipeline.

    -job_topup       :   Another special initialization mode when only jobs are created - no other structural changes to the pipeline are acted upon.

    -hive_force_init :   If set to 1, forces the (re)creation of the hive database even if a previous version of it is present in the server.</code></pre>

<h1 id="LICENSE">LICENSE</h1>

<pre><code>    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute

    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
    You may obtain a copy of the License at

         http://www.apache.org/licenses/LICENSE-2.0

    Unless required by applicable law or agreed to in writing, software distributed under the License
    is distributed on an &quot;AS IS&quot; BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and limitations under the License.</code></pre>

<h1 id="CONTACT">CONTACT</h1>

<pre><code>    Please subscribe to the Hive mailing list:  http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users  to discuss Hive-related questions or to be notified of our updates</code></pre>


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