galaxyproject / pulsar

Distributed job execution application built for Galaxy
https://pulsar.readthedocs.io
Apache License 2.0
37 stars 50 forks source link

Poster Dependency for pulsar. #248

Closed cibinsb closed 3 years ago

cibinsb commented 3 years ago

I'm trying to install Pulsar from source, after successful installation and starting the pulsar server using ./run.sh command. The following error is  thrown on the console when galaxy jobs are submitted to pulsar.

raise ImportError(POSTER_UNAVAILABLE_MESSAGE)
ImportError: Pulsar configured to use poster module - but it is unavailable. Please install poster.

however, poster package is not available for python 3.   Pulsar and galaxy are running on ubuntu 20.04 with python3.8.5

Galaxy job_conf.xml

<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is
     configured by default (if there is no explicit config). -->
<job_conf>
    <plugins>
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
        <plugin id="pulsar_runner" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner">
        <param id="galaxy_url">http://0.0.0.0:8080/</param>
        </plugin>
    </plugins>
    <destinations default="local">
        <destination id="local" runner="local"/>
        <destination id="pulsar" runner="pulsar_runner">
            <param id="url">http://localhost:8913/</param>
            <param id="default_file_action">remote_transfer</param>
            <param id="dependency_resolution">remote</param>
            <param id="remote_metadata">False</param>
            <param id="rewrite_parameters">True</param>
            <param id="transport">curl</param>
            <param id="manager">_default_</param>
        </destination>
    </destinations>
        <tools>
        <tool id="tp_tail_tool" destination="pulsar"/>
        <tool id="tp_cut_tool" destination="pulsar"/>
        <tool id="wc_gnu" destination="pulsar"/>
        <tool id="fastqc" destination="pulsar" />
        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1" destination="pulsar"/>
        <tool id="toolshed.g2.bx.psu.edu/repos/mnhn65mo/csv_to_tabular/csv2tab_R/0.1" destination="pulsar"/>
     </tools>
</job_conf>
cibinsb commented 3 years ago

Fixed the issue by installing pycurl, thanks to the suggestions from galaxy/admin