Mercurial > repos > iuc > ega_download_client

changeset 6:0b67eabbc6e4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3ac2b4221e3aa5de4cef9f453ac1a7425ce130c2
author iuc
date Thu, 28 Sep 2023 12:07:04 +0000
parents ce69320f0845
children e1893fd12fee
files README.md README.rst pyega3.xml test-data/filelist_EGAD00001003338.tabular
diffstat 4 files changed, 32 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Fri Apr 07 21:48:09 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-# PyEGA3
-
-## Set up user credentials on Galaxy
-
-To enable users to set their credentials for this tool,
-make sure the file `config/user_preferences_extra.yml` has the following section:
-
-```
-    ega_account:
-        description: Your EGA (European Genome Archive) account
-        inputs:
-            - name: username
-              label: Username
-              type: text
-              required: False
-            - name: password
-              label: Password
-              type:  password
-              required: False
-```
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Sep 28 12:07:04 2023 +0000
@@ -0,0 +1,22 @@
+PyEGA3
+======
+
+Set up user credentials on Galaxy
+---------------------------------
+
+To enable users to set their credentials for this tool, make sure the
+file ``config/user_preferences_extra.yml`` has the following section:
+
+::
+
+       ega_account:
+           description: Your EGA (European Genome Archive) account
+           inputs:
+               - name: username
+                 label: Username
+                 type: text
+                 required: False
+               - name: password
+                 label: Password
+                 type:  password
+                 required: False
--- a/pyega3.xml	Fri Apr 07 21:48:09 2023 +0000
+++ b/pyega3.xml	Thu Sep 28 12:07:04 2023 +0000
@@ -234,6 +234,12 @@
     <help><![CDATA[
 The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets.
 
+.. class:: Warning mark
+
+	Data is stored unencrypted on the user's Galaxy account. Confidential data from the EGA could be left unprotected when uploaded to a public Galaxy server.
+	Make sure to read the EGA Data Access Agreement ([DAA](https://ega-archive.org/files/Example_DAA.doc)) before uploading any data to Galaxy from the EGA.
+	If this applies to you, we recommend you follow [this link](https://github.com/elixir-europe/GalaxySensitiveData-ELIXIR_IS) for updates on encrypted data at rest.
+
 If you have an EGA account, you can set your EGA credentials in the user preferences menu of Galaxy. Otherwise, default EGA credentials with access to an example dataset will be used.
 
 pyEGA3 uses the EGA Data API and has several key features:
--- a/test-data/filelist_EGAD00001003338.tabular	Fri Apr 07 21:48:09 2023 +0000
+++ b/test-data/filelist_EGAD00001003338.tabular	Thu Sep 28 12:07:04 2023 +0000
@@ -81,3 +81,7 @@
 EGAF00007553559	1	2426228900	66bb08a031ff66c8c03ee9917be53fcf	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes_only_chr1and2.vcf.gz
 EGAF00007553560	1	2691732	26d41f1a09671c834fd7b4eaac3f1a67	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes.vcf.gz.tbi
 EGAF00007553561	1	434009	357abb1556367d5c096cd54801a5e783	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes_only_chr1and2.vcf.gz.tbi
+EGAF00008047669	1	14585114453	1377526fc26a58294635ba48edc35535	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.redo.genotypes.bcf
+EGAF00008047670	1	2260066	638b9524583d585c5276eed6e1f198b0	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.redo.genotypes.bcf.csi
+EGAF00008047671	1	2053513514	a6d323bb194eac03e7112c243aeef5d3	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.redo.genotypes_only_chr1and2.bcf
+EGAF00008047672	1	353029	ae95e52511a6a28b9b01d2beabdc59dd	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.redo.genotypes_only_chr1and2.bcf.csi