Add 6 new tools to cpt.yaml #776
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Add 5 tools, remove 2 tools
added defense_finder
bgruening
reviewed
Aug 30, 2024
| @@ -64,18 +64,10 @@ tools: | |||
| owner: cpt | |||
| tool_panel_section_label: Annotation | |||
|
|
|||
| - name: cpt_intersect_adjacent | |||
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We can not remove tools, they need to stay for reproducibility ... we could hide them if this is useful.
Please let them listed here and add a comment that they are deprecated.
bgruening
reviewed
Aug 30, 2024
cpt.yaml
Outdated
| tool_panel_section_label: Annotation | ||
|
|
||
| - name: phageterm | ||
| owner: mmonot |
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We need to review those tools before we can merge them.
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Can you point me maybe to the github repo of those tools?
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https://github.com/avilella/phageterm <- is a fork
The only reference on github is https://github.com/TAMU-CPT/galaxy-tools/blob/c43f5a7706fb64615b7c050a5a9e5fc20ca33873/tool_conf.xml.old#L76 ... any reason you have hidden it on your instance?
I think I found the latest version https://gitlab.pasteur.fr/vlegrand/ptv/-/tree/master
But the Galaxy wrapper is 6 years old and has not been updated. I could not find the source on github, the source in the TS is insecure and needs updates.
|
Hi Bjoern,
Here are the repos for our tools:
cpt_protein_blast_grouping :: https://github.com/TAMU-CPT/CPT-ToolshedSource/tree/main/cpt_protein_blast_grouping
cpt_prophage_relatedness :: https://github.com/TAMU-CPT/CPT-ToolshedSource/tree/main/cpt_prophage_relatedness
cpt_intersect_adj :: https://github.com/TAMU-CPT/CPT-ToolshedSource/tree/main/cpt_intersect_adj
The other three tools are from other authors but would also be useful for Phage Galaxy. These tools all worked on Curtis’ Galaxy testbed. Let us know if you need any edits. I will also revert the deletions of those two other tools, should I just add a ## comment line under each of those to state they are deprecated?
Thanks,
Jason.
From: Björn Grüning ***@***.***>
Sent: Friday, August 30, 2024 1:20 PM
To: usegalaxy-eu/usegalaxy-eu-tools ***@***.***>
Cc: jasonjgill ***@***.***>; Author ***@***.***>
Subject: Re: [usegalaxy-eu/usegalaxy-eu-tools] Add 6 new tools to cpt.yaml (PR #776)
@ bgruening commented on this pull request. In cpt. yaml: > @@ -127,3 +119,27 @@ tools: - name: cpt_fasta_translate owner: cpt tool_panel_section_label: Annotation + + - name: cpt_protein_blast_grouping + owner: cpt + tool_panel_section_label:
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@bgruening commented on this pull request.
________________________________
In cpt.yaml<https://urldefense.com/v3/__https:/github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/776*discussion_r1739226709__;Iw!!KwNVnqRv!CJMb5yfl26KVHlzC2-HZFAmZsqUj6OwunK9OFHMlKm94u3_SammvyB9ckINRD9_hDV3yMvNXBIEmNUQysPuUnBCp8OI$>:
@@ -127,3 +119,27 @@ tools:
- name: cpt_fasta_translate
owner: cpt
tool_panel_section_label: Annotation
+
+ - name: cpt_protein_blast_grouping
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: cpt_prophage_relatedness
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: cpt_intersect_adj
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: phageterm
+ owner: mmonot
Can you point me maybe to the github repo of those tools?
—
Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/776*discussion_r1739226709__;Iw!!KwNVnqRv!CJMb5yfl26KVHlzC2-HZFAmZsqUj6OwunK9OFHMlKm94u3_SammvyB9ckINRD9_hDV3yMvNXBIEmNUQysPuUnBCp8OI$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AKIFQTX5P66KXZY74WBXZNLZUCZVVAVCNFSM6AAAAABNM22G5WVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDENZTGIZTQNRQG4__;!!KwNVnqRv!CJMb5yfl26KVHlzC2-HZFAmZsqUj6OwunK9OFHMlKm94u3_SammvyB9ckINRD9_hDV3yMvNXBIEmNUQysPuUtNa_PT0$>.
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bgruening
reviewed
Sep 1, 2024
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@jasonjgill I tried to find the source of the tools, see my comments inline.
I'm not concerned about functionality. I trust you all when you say those tools are useful. My problem is with sustainability and security. When those wrappers are not maintained over time, do not have tests, or do not adhere to basic security needs of a public Galaxy server, I have problems to install them.
Thats why I recommend to contribute your tools to IUC as well. There we have a review process, rigorous testing and bots that help us maintaining the warppers.
cpt.yaml
Outdated
| tool_panel_section_label: Annotation | ||
|
|
||
| - name: phageterm | ||
| owner: mmonot |
There was a problem hiding this comment.
https://github.com/avilella/phageterm <- is a fork
The only reference on github is https://github.com/TAMU-CPT/galaxy-tools/blob/c43f5a7706fb64615b7c050a5a9e5fc20ca33873/tool_conf.xml.old#L76 ... any reason you have hidden it on your instance?
I think I found the latest version https://gitlab.pasteur.fr/vlegrand/ptv/-/tree/master
But the Galaxy wrapper is 6 years old and has not been updated. I could not find the source on github, the source in the TS is insecure and needs updates.
cpt.yaml
Outdated
|
|
||
| - name: phagetermvirome | ||
| owner: bioit_sciensano | ||
| tool_panel_section_label: Annotation |
There was a problem hiding this comment.
This one also seems to be https://gitlab.pasteur.fr/vlegrand/ptv/-/tree/master
The previous PhageTerm program (single phage analysis only) is still available at https://sourceforge.net/projects/phageterm/ (for versions <3.0.0)
But also no Galaxy wrapper in github/gitlab.
The wrapper in the TS looks ok, a few things can be improved.
cpt.yaml
Outdated
| tool_panel_section_label: Annotation | ||
|
|
||
| - name: defense_finder | ||
| owner: rplanel |
There was a problem hiding this comment.
That one looks ok, I found the wrapper and it looks like a good quality.
|
Hi Bjoern,
I have cc'd Curtis who can address issues in our repo. The third-party tools are outside of our control, I guess all we could do would be to try to update them and see if they will merge our changes. We can drop tools from the PR for now if needed, the priority for us are the 3 CPT tools. Getting into IUC is our eventual plan, it's mostly an issue of available resources. We have a new worker we might be able to task with this.
Thanks,
Jason.
Jason Gill
Associate Professor
Dept. of Animal Science
Texas A&M University
Sent via mobile.
On Sep 1, 2024 9:45 AM, Björn Grüning ***@***.***> wrote:
@ bgruening commented on this pull request. @jasonjgill I tried to find the source of the tools, see my comments inline. I'm not concerned about functionality. I trust you all when you say those tools are useful. My problem is with sustainability
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@bgruening commented on this pull request.
@jasonjgill<https://urldefense.com/v3/__https://github.com/jasonjgill__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNRGjAnt4$> I tried to find the source of the tools, see my comments inline.
I'm not concerned about functionality. I trust you all when you say those tools are useful. My problem is with sustainability and security. When those wrappers are not maintained over time, do not have tests, or do not adhere to basic security needs of a public Galaxy server, I have problems to install them.
Thats why I recommend to contribute your tools to IUC as well. There we have a review process, rigorous testing and bots that help us maintaining the warppers.
________________________________
In cpt.yaml<https://urldefense.com/v3/__https://github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/776*discussion_r1740122805__;Iw!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqN8Bk7uV0$>:
+
+ - name: cpt_prophage_relatedness
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: cpt_intersect_adj
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: phageterm
+ owner: mmonot
+ tool_panel_section_label: Annotation
+
+ - name: phagetermvirome
+ owner: bioit_sciensano
+ tool_panel_section_label: Annotation
This one also seems to be https://gitlab.pasteur.fr/vlegrand/ptv/-/tree/master<https://urldefense.com/v3/__https://gitlab.pasteur.fr/vlegrand/ptv/-/tree/master__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNAkdnVL0$>
The previous PhageTerm program (single phage analysis only) is still available at https://sourceforge.net/projects/phageterm/<https://urldefense.com/v3/__https://sourceforge.net/projects/phageterm/__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNNtyzbM8$> (for versions <3.0.0)
But also no Galaxy wrapper in github/gitlab.
The wrapper in the TS looks ok, a few things can be improved.
________________________________
In cpt.yaml<https://urldefense.com/v3/__https://github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/776*discussion_r1740126241__;Iw!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNxxrkjIM$>:
+ tool_panel_section_label: Annotation
+
+ - name: cpt_intersect_adj
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: phageterm
+ owner: mmonot
+ tool_panel_section_label: Annotation
+
+ - name: phagetermvirome
+ owner: bioit_sciensano
+ tool_panel_section_label: Annotation
+
+ - name: defense_finder
+ owner: rplanel
That one looks ok, I found the wrapper and it looks like a good quality.
________________________________
In cpt.yaml<https://urldefense.com/v3/__https://github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/776*discussion_r1740122799__;Iw!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqN_cRG9WQ$>:
@@ -127,3 +119,27 @@ tools:
- name: cpt_fasta_translate
owner: cpt
tool_panel_section_label: Annotation
+
+ - name: cpt_protein_blast_grouping
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: cpt_prophage_relatedness
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: cpt_intersect_adj
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: phageterm
+ owner: mmonot
https://github.com/avilella/phageterm<https://urldefense.com/v3/__https://github.com/avilella/phageterm__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNSia5iMs$> <- is a fork
The only reference on github is https://github.com/TAMU-CPT/galaxy-tools/blob/c43f5a7706fb64615b7c050a5a9e5fc20ca33873/tool_conf.xml.old#L76<https://urldefense.com/v3/__https://github.com/TAMU-CPT/galaxy-tools/blob/c43f5a7706fb64615b7c050a5a9e5fc20ca33873/tool_conf.xml.old*L76__;Iw!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNN2uONbA$> ... any reason you have hidden it on your instance?
I think I found the latest version https://gitlab.pasteur.fr/vlegrand/ptv/-/tree/master<https://urldefense.com/v3/__https://gitlab.pasteur.fr/vlegrand/ptv/-/tree/master__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNAkdnVL0$>
But the Galaxy wrapper is 6 years old and has not been updated. I could not find the source on github, the source in the TS is insecure and needs updates.
—
Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/776*pullrequestreview-2274402801__;Iw!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqN0W826sY$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AKIFQTQAAB5DQVIUEWGA543ZUMSBFAVCNFSM6AAAAABNM22G5WVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDENZUGQYDEOBQGE__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqN7PySJTk$>.
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Hi Bjoern,
If we drop phageterm, phagetermvirome and defense_finder from the PR, are you OK with installing the other tools? The CPT tools are the ones we need the most.
Thanks,
Jason.
________________________________
From: Björn Grüning ***@***.***>
Sent: Sunday, September 1, 2024 9:45 AM
To: usegalaxy-eu/usegalaxy-eu-tools ***@***.***>
Cc: jasonjgill ***@***.***>; Mention ***@***.***>
Subject: Re: [usegalaxy-eu/usegalaxy-eu-tools] Add 6 new tools to cpt.yaml (PR #776)
@ bgruening commented on this pull request. @jasonjgill I tried to find the source of the tools, see my comments inline. I'm not concerned about functionality. I trust you all when you say those tools are useful. My problem is with sustainability
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@bgruening commented on this pull request.
@jasonjgill<https://urldefense.com/v3/__https://github.com/jasonjgill__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNRGjAnt4$> I tried to find the source of the tools, see my comments inline.
I'm not concerned about functionality. I trust you all when you say those tools are useful. My problem is with sustainability and security. When those wrappers are not maintained over time, do not have tests, or do not adhere to basic security needs of a public Galaxy server, I have problems to install them.
Thats why I recommend to contribute your tools to IUC as well. There we have a review process, rigorous testing and bots that help us maintaining the warppers.
________________________________
In cpt.yaml<https://urldefense.com/v3/__https://github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/776*discussion_r1740122805__;Iw!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqN8Bk7uV0$>:
+
+ - name: cpt_prophage_relatedness
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: cpt_intersect_adj
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: phageterm
+ owner: mmonot
+ tool_panel_section_label: Annotation
+
+ - name: phagetermvirome
+ owner: bioit_sciensano
+ tool_panel_section_label: Annotation
This one also seems to be https://gitlab.pasteur.fr/vlegrand/ptv/-/tree/master<https://urldefense.com/v3/__https://gitlab.pasteur.fr/vlegrand/ptv/-/tree/master__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNAkdnVL0$>
The previous PhageTerm program (single phage analysis only) is still available at https://sourceforge.net/projects/phageterm/<https://urldefense.com/v3/__https://sourceforge.net/projects/phageterm/__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNNtyzbM8$> (for versions <3.0.0)
But also no Galaxy wrapper in github/gitlab.
The wrapper in the TS looks ok, a few things can be improved.
________________________________
In cpt.yaml<https://urldefense.com/v3/__https://github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/776*discussion_r1740126241__;Iw!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNxxrkjIM$>:
+ tool_panel_section_label: Annotation
+
+ - name: cpt_intersect_adj
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: phageterm
+ owner: mmonot
+ tool_panel_section_label: Annotation
+
+ - name: phagetermvirome
+ owner: bioit_sciensano
+ tool_panel_section_label: Annotation
+
+ - name: defense_finder
+ owner: rplanel
That one looks ok, I found the wrapper and it looks like a good quality.
________________________________
In cpt.yaml<https://urldefense.com/v3/__https://github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/776*discussion_r1740122799__;Iw!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqN_cRG9WQ$>:
@@ -127,3 +119,27 @@ tools:
- name: cpt_fasta_translate
owner: cpt
tool_panel_section_label: Annotation
+
+ - name: cpt_protein_blast_grouping
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: cpt_prophage_relatedness
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: cpt_intersect_adj
+ owner: cpt
+ tool_panel_section_label: Annotation
+
+ - name: phageterm
+ owner: mmonot
https://github.com/avilella/phageterm<https://urldefense.com/v3/__https://github.com/avilella/phageterm__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNSia5iMs$> <- is a fork
The only reference on github is https://github.com/TAMU-CPT/galaxy-tools/blob/c43f5a7706fb64615b7c050a5a9e5fc20ca33873/tool_conf.xml.old#L76<https://urldefense.com/v3/__https://github.com/TAMU-CPT/galaxy-tools/blob/c43f5a7706fb64615b7c050a5a9e5fc20ca33873/tool_conf.xml.old*L76__;Iw!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNN2uONbA$> ... any reason you have hidden it on your instance?
I think I found the latest version https://gitlab.pasteur.fr/vlegrand/ptv/-/tree/master<https://urldefense.com/v3/__https://gitlab.pasteur.fr/vlegrand/ptv/-/tree/master__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqNAkdnVL0$>
But the Galaxy wrapper is 6 years old and has not been updated. I could not find the source on github, the source in the TS is insecure and needs updates.
—
Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/776*pullrequestreview-2274402801__;Iw!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqN0W826sY$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AKIFQTQAAB5DQVIUEWGA543ZUMSBFAVCNFSM6AAAAABNM22G5WVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDENZUGQYDEOBQGE__;!!KwNVnqRv!H1w7o4CxfBrt_85mrD2AgxWW6VteWFZWpwkccbEZnjYSlRjUhlEBQVJdmuvgQRlAbNG3OQ3g0qbA0x_18nqN7PySJTk$>.
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Added back cpt_intersect_adjacent and cpt_related_genomes_prot for repeatability issues with comments, removed phageterm, phagetermvirome and defense_finder, will deal with these in a future PR. Net change is adding 3 new CPT tools.
|
Made a new commit to add back the 2 deleted tools (with comments) and removed the third-party tools. Net change now is just the 3 new CPT tools. |
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Adds 3 new CPT phage tools, deletes 2 deprecated CPT tools, adds 3 new useful phage tools from the toolshed.