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TAMU-CPT / galaxy-tools

CPT's Galaxy Tools
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Add CRISPR-related tools into Galaxy #22

Open jrr-cpt opened 6 years ago

jrr-cpt commented 6 years ago

CRISPR-finder for finding repeats: http://crispr.i2bc.paris-saclay.fr/Server/ PHASTER for finding the proteins: http://phaster.ca/

MoffMade commented 6 years ago

Neither of these packages are on the Galaxy Toolshed, so a wrapper would need to be written for them. I am looking to find an available executable for each tool and will start building and testing wrappers.

I did find a "CRISPR Recoginition Tool" available on the Toolshed (http://www.room220.com/crt/). Would this be useful? It looks as though CRISPR-finder was a competitor/replacement tool for CRT from a quick literature search.

jrr-cpt commented 6 years ago

The CRISPR-finder tool was recommended as used by the Bondy-Denomy lab. We should use that version, or move ahead with the later version that also incorporates looking for Cas proteins: https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index

If the wrappers will take a couple months, but the CRT can be available right away, then install and I can run a couple genomes through to see the output in the meantime.

2018-08-22 15:48 GMT-05:00 Cory Maughmer notifications@github.com:

Neither of these packages are on the Galaxy Toolshed, so a wrapper would need to be written for them. I am looking to find an available executable for each tool and will start building and testing wrappers.

I did find a "CRISPR Recoginition Tool" available on the Toolshed ( http://www.room220.com/crt/ https://urldefense.proofpoint.com/v2/url?u=http-3A__www.room220.com_crt_&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=pwOSL5nLf8L4CDL1AitBiPq5upb7j6pJnAxLdnfHyMY&m=Bn0zp2yQhmuSSSDp0_iwYExsAdcrGF1Q1n-qvyxKlP4&s=u7LSHy-6UTJlcLzvvuS_4yBS6yCq89UQDG9TPQfjxH0&e=). Would this be useful? It looks as though CRISPR-finder was a competitor/replacement tool for CRT from a quick literature search.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_TAMU-2DCPT_galaxy-2Dtools_issues_22-23issuecomment-2D415174564&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=pwOSL5nLf8L4CDL1AitBiPq5upb7j6pJnAxLdnfHyMY&m=Bn0zp2yQhmuSSSDp0_iwYExsAdcrGF1Q1n-qvyxKlP4&s=APe9yW6InrH1zH6MML-NnErPG4hXJhcYFlqRBPwkrEw&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AlF7Zh0h08qhodBqQ5OBaIrTqcCJQGgNks5uTcOjgaJpZM4V4p7J&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=pwOSL5nLf8L4CDL1AitBiPq5upb7j6pJnAxLdnfHyMY&m=Bn0zp2yQhmuSSSDp0_iwYExsAdcrGF1Q1n-qvyxKlP4&s=ioDxaYcfUQyXWS6N6JngvWVhE5ZcC07tn40-H0dkxFs&e= .

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MoffMade commented 6 years ago

It looks like the CRISPR Cas Finder tool is available for download, so a wrapper can be started for this one. I was unable to find downloadable tools for CRISPR-Finder and PHASTER, so we'd need to reach out to the owners for a tool executable before they can be made available in Galaxy.

I'll add the CRISPR Cas Finder tool to my list of tools to wrap

MoffMade commented 6 years ago

CRISPR CAS Finder retrieved from https://crisprcas.i2bc.paris-saclay.fr/Home/Download

jrr-cpt commented 5 years ago

Let's install the "CRISPR Recoginition Tool" available on the Toolshed (http://www.room220.com/crt/) to use until the CRISPR-Cas Finder gets wrapped.

I gave @MoffMade the most up-to-date anti-CRISPR database (with the May 2018 sequences added by me in Galaxy) from cefg.uestc.edu.cn/anti-CRISPRdb/

RiversDong commented 5 years ago

Here is a standalone version tool for annotating Cas proteins, Cas loci, and corresponding (sub)types. https://github.com/RiversDong/CasLocusAnno. CasLocusAnno, capable of annotating Cas proteins, cas loci and their (sub)types ~28 seconds following the whole proteome sequence submission