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PySCENIC: Use bioconda dependency now available #337

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PySCENIC: Use bioconda dependency now available #337

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Use bioconda dependency now available
pcm32 Nov 1, 2024
5a868d9
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pcm32 Nov 1, 2024
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1 change: 1 addition & 0 deletions tools/tertiary-analysis/pyscenic/.shed.yml
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Expand Up @@ -2,6 +2,7 @@ categories:
- Transcriptomics
- RNA
- Sequence Analysis
- Single Cell
description: "PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/"
long_description: |
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering)
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4 changes: 1 addition & 3 deletions tools/tertiary-analysis/pyscenic/macros.xml
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Expand Up @@ -2,9 +2,7 @@
<token name="@TOOL_VERSION@">0.12.1</token>
<xml name="requirements">
<requirements>
<container type="docker">
aertslab/pyscenic:@TOOL_VERSION@
</container>
<requirement type="package" version="@TOOL_VERSION@">pyscenic</requirement>
</requirements>
</xml>
<xml name="citations">
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2 changes: 1 addition & 1 deletion tools/tertiary-analysis/pyscenic/pyscenic_aucell.xml
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@@ -1,4 +1,4 @@
<tool id="pyscenic_aucell" name="PySCENIC AUCell" profile="21.09" version="@TOOL_VERSION@+galaxy0">
<tool id="pyscenic_aucell" name="PySCENIC AUCell" profile="21.09" version="@TOOL_VERSION@+galaxy1">
<description>calculates AUCell to find relevant regulons/gene sets</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/tertiary-analysis/pyscenic/pyscenic_binarize_aucell.xml
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@@ -1,4 +1,4 @@
<tool id="pyscenic_binarize" name="PySCENIC Binarize AUCell" profile="21.09" version="@TOOL_VERSION@+galaxy0">
<tool id="pyscenic_binarize" name="PySCENIC Binarize AUCell" profile="21.09" version="@TOOL_VERSION@+galaxy1">
<description>defines AUCell thresholds and tags cells as passing it or not</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/tertiary-analysis/pyscenic/pyscenic_ctx.xml
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@@ -1,4 +1,4 @@
<tool id="pyscenic_ctx" name="PySCENIC CTX" profile="21.09" version="@TOOL_VERSION@+galaxy0">
<tool id="pyscenic_ctx" name="PySCENIC CTX" profile="21.09" version="@TOOL_VERSION@+galaxy1">
<description>
computes active regulons based on a gene regulatory network
</description>
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2 changes: 1 addition & 1 deletion tools/tertiary-analysis/pyscenic/pyscenic_grn.xml
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@@ -1,4 +1,4 @@
<tool id="pyscenic_grn" name="PySCENIC GRN" version="@TOOL_VERSION@+galaxy0" profile="21.09">
<tool id="pyscenic_grn" name="PySCENIC GRN" version="@TOOL_VERSION@+galaxy1" profile="21.09">
<description>infers gene regulatory networks</description>
<macros>
<import>macros.xml</import>
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