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Lucille Delisle lldelisle EPFL Lausanne, Switzerland

deeptools/pyGenomeTracks 525

python module to plot beautiful and highly customizable genome browser tracks

galaxyproject/training-material 217

A collection of Galaxy-related training material

deeptools/HiCExplorer 143

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

bxlab/bx-python 110

Tools for manipulating biological data, particularly multiple sequence alignments

lldelisle/analysePeaks 1

A package to compare your peaks for ChIP/CUT&RUN/ATAC... between them

aurHin/4C_analyses 0

How to average 4C data from two biological replicates?

lldelisle/ansible-proftpd 0

Ansible role for installing and configuring ProFTPD for Galaxy

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Lucille Delisle

commit sha cdfa82e5460ece0661485707658178a5a1c83d73

add no arch generic

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PR opened bioconda/bioconda-recipes

Add Fiji morpholibj

Add a recipe for a fiji plugin. I am not sure if my test is good.

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

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[ci skip] Merge PR 30867 Merge PR #30867, commits were: * drop - change snakemake to snakemake-minimal (#31108) * snakemake to snakemake-minimal attempt to reduce memory * reset build number to 0 * Update drop to 1.1.0

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Update upimapi to 1.6.0 (#31130) * Update upimapi to 1.6.0 * Update meta.yaml Co-authored-by: João Sequeira <maildosequeira@gmail.com>

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Pull request review commentgalaxyproject/tools-iuc

update download_idr

                 <param name="id_dataset_omero" type="integer" min = "0" value = "9059" label="Dataset ID"/>             </when>         </conditional>-        <param name="channel" type="text"-        label="Name of the channel to download"-        help="For all image IDs only the specified channel will be downloaded. If left empty, the first channel (whatever this is) will be downloaded by default." />-        <param name="z_section" type="integer" value="0" min="0"-        label="z-plane of images to download" />-        <param name="frame" type="integer" value="0" min="0"-        label="Image frame to download" />-        <conditional name="clip_image">-            <param name="select" type="select"-            label="Limit the download to a selected region of the image?">-                <option value="">No, download the entire image plane</option>-                <option value="--rectangle">Specify a region using its upper-left corner</option>-                <option value="--center">Specify a width x height region around a central point</option>++        <conditional name="image_region">+            <param name="original" type="select" label="Which images do you want to download?">+                <option value="TIFF">Exported TIFF (single channel, single stack)</option>+                <option value="original">Original file (file uploaded to omero, only available for private instances)</option>             </param>-            <when value="" />-            <when value="--rectangle">-                <expand macro="region_spec" />-            </when>-            <when value="--center">-                <expand macro="region_spec" pos="center" />+            <when value="original"/>+            <when value="TIFF">

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explicit default of original

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update version

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pull request commentgalaxyproject/tools-iuc

update download_idr

Why should I update the profile? If it is compatible with 18.09 we should keep it, no?

lldelisle

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pull request commentgalaxyproject/tools-iuc

update download_idr

Do you know to what the tool version 0.43 stand for?

lldelisle

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Pull request review commentgalaxyproject/tools-iuc

update download_idr

             </conditional>             <param name="source" value="dataset" />             <param name="id_spec" value="ids.txt" />-            <param name="channel" value="PCNT" />-            <conditional name="clip_image">-                <param name="select" value="--rectangle" />-                <param name="x_coord" value="3" />-                <param name="y_coord" value="3" />-                <param name="width" value="5" />-                <param name="height" value="5" />+            <conditional name="image_region">+                <param name="original" value="TIFF"/>            <param name="channel" value="PCNT" />

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fix wrong back to line

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fix typo

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linting

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Pull request review commentgalaxyproject/tools-iuc

update download_idr

                 <param name="id_dataset_omero" type="integer" min = "0" value = "9059" label="Dataset ID"/>             </when>         </conditional>-        <param name="channel" type="text"-        label="Name of the channel to download"-        help="For all image IDs only the specified channel will be downloaded. If left empty, the first channel (whatever this is) will be downloaded by default." />-        <param name="z_section" type="integer" value="0" min="0"-        label="z-plane of images to download" />-        <param name="frame" type="integer" value="0" min="0"-        label="Image frame to download" />-        <conditional name="clip_image">-            <param name="select" type="select"-            label="Limit the download to a selected region of the image?">-                <option value="">No, download the entire image plane</option>-                <option value="--rectangle">Specify a region using its upper-left corner</option>-                <option value="--center">Specify a width x height region around a central point</option>++        <conditional name="image_region">+            <param name="original" type="select" label="Which images do you want to download?">+                <option value="TIFF">Exported TIFF (single channel, single stack)</option>+                <option value="original">Original file (file uploaded to omero, only available for private instances)</option>             </param>-            <when value="" />-            <when value="--rectangle">-                <expand macro="region_spec" />-            </when>-            <when value="--center">-                <expand macro="region_spec" pos="center" />+            <when value="original"/>+            <when value="TIFF">

I put it first, I thought this would me it is the default.

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PR opened galaxyproject/tools-iuc

update download_idr

FOR CONTRIBUTOR:

  • [X] - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • [X] - License permits unrestricted use (educational + commercial)
  • [ ] - This PR adds a new tool or tool collection
  • [X] - This PR updates an existing tool or tool collection
  • [ ] - This PR does something else (explain below)

This allow to download original images in galaxy. This is not usable in idr but in private instances... Then I don't know how to do a proper test...

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update error message in test

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use a single requirement file for CI

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update version of macOS

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add python 3.9

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Merge pull request #372 from deeptools/changeOSXAzure Change osx azure

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Merge branch 'develop' of https://github.com/deeptools/pyGenomeTracks into messageRTF

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use a single requirement file for CI

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update version of macOS

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add python 3.9

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Merge pull request #372 from deeptools/changeOSXAzure Change osx azure

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add test

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Merge branch 'develop' of https://github.com/deeptools/pyGenomeTracks into fixMatrixPlotOutsideRange

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PR opened deeptools/pyGenomeTracks

Change osx azure

Update CI:

  • use a single file with all requirements
  • Use last version of OSX
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PR opened deeptools/pyGenomeTracks

use more explicit error message for rtf

Related to #369

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