Mercurial > repos > iuc > nonpareil
changeset 2:cef64c36c89e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 0b535bf15f4bb0110f599c1af9b1dc1c66302899
| author | iuc |
|---|---|
| date | Tue, 12 Mar 2024 08:50:50 +0000 |
| parents | 45210df786b9 |
| children | |
| files | README.rst macros.xml nonpareil.xml |
| diffstat | 3 files changed, 20 insertions(+), 29 deletions(-) [+] |
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--- a/README.rst Wed Jul 27 09:26:36 2022 +0000 +++ b/README.rst Tue Mar 12 08:50:50 2024 +0000 @@ -1,29 +1,7 @@ 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> - <plugins> - <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> - </plugins> - <handlers> - <handler id="main"/> - </handlers> - <destinations> - <destination id="local" runner="local"> - <env id="NONPAREIL_MAX_MEMORY">1024</env> - </destination> - </destinations> -</job_conf> -``` - - - +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.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 12 08:50:50 2024 +0000 @@ -0,0 +1,14 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">nonpareil</requirement> + </requirements> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">nonpareil</xref> + </xrefs> + </xml> + <token name="@TOOL_VERSION@">3.1.1</token> +</macros> \ No newline at end of file
--- a/nonpareil.xml Wed Jul 27 09:26:36 2022 +0000 +++ b/nonpareil.xml Tue Mar 12 08:50:50 2024 +0000 @@ -1,11 +1,10 @@ <tool id="nonpareil" name="Nonpareil" version="@TOOL_VERSION@.1" profile="21.01"> <description>to estimate average coverage and generate Nonpareil curves</description> <macros> - <token name="@TOOL_VERSION@">3.1.1</token> + <import>macros.xml</import> </macros> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">nonpareil</requirement> - </requirements> + <expand macro="xrefs"/> + <expand macro="requirements"/> <version_command>nonpareil -V</version_command> <command detect_errors="exit_code"> <![CDATA[