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Repository nonpareil
Name: nonpareil
Owner: iuc
Synopsis: Estimate average coverage in metagenomic datasets
Nonpareil uses the redundancy of the reads in metagenomic datasets to estimate the average 
coverage and predict the amount of sequences that will be required to achieve "nearly complete coverage".
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/nonpareil
Type: unrestricted
Revision: 1:45210df786b9
This revision can be installed: True
Times cloned / installed: 480

Repository README files - may contain important installation or license information

Nonpareil memory usage

By default, this tool is configured to limit the memory consumption to 1024 Mib.

Ideally this value should be larger than the sequences to analyze (discarding non-sequence elements like headers or quality). This is particularly important when running in multiple cores. This value is approximated. Maximum value in this version: 4194303.

You can set the NONPAREIL_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file:

``` <?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>

System Message: WARNING/2 (<string>, line 10); backlink

Inline literal start-string without end-string.

System Message: ERROR/3 (<string>, line 14)

Unexpected indentation.
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>

System Message: WARNING/2 (<string>, line 16)

Definition list ends without a blank line; unexpected unindent.

</plugins> <handlers>

System Message: ERROR/3 (<string>, line 18)

Unexpected indentation.
<handler id="main"/>

System Message: WARNING/2 (<string>, line 19)

Block quote ends without a blank line; unexpected unindent.

</handlers> <destinations>

System Message: ERROR/3 (<string>, line 21)

Unexpected indentation.
<destination id="local" runner="local">
<env id="NONPAREIL_MAX_MEMORY">1024</env>

System Message: WARNING/2 (<string>, line 23)

Definition list ends without a blank line; unexpected unindent.

</destination>

System Message: WARNING/2 (<string>, line 24)

Block quote ends without a blank line; unexpected unindent.

</destinations>

System Message: WARNING/2 (<string>, line 25)

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</job_conf> ```

System Message: WARNING/2 (<string>, line 25); backlink

Inline literal start-string without end-string.

System Message: WARNING/2 (<string>, line 25); backlink

Inline interpreted text or phrase reference start-string without end-string.

Contents of this repository

Name Description Version Minimum Galaxy Version
to estimate average coverage and generate Nonpareil curves 3.1.1.1 21.01

Categories
Metagenomics - Tools enabling the study of metagenomes