RepeatModeler and RepeatMasker

[dmacguigan]

Hello,

I would like to request the installation of RepeatModeler (https://github.com/Dfam-consortium/RepeatModeler, http://www.repeatmasker.org/RepeatModeler/) and RepeatMasker (https://www.repeatmasker.org/RepeatMasker/). I have tried to install this software myself, but have run into issues during configuration, particularly with the Perl dependencies.

This software would be very useful for a number of labs in the Biological Sciences department. Masking repetitive elements in genomes is a crucial prerequisite for functional annotation and many other analyses.

Thanks, Dan

[dsajdak]

@dmacguigan it does not look like you're using CCR's new modules. Please see here for instructions: https://docs.ccr.buffalo.edu/en/latest/software/modules/ Since these are contained in the Easy Build recipe database, you can try building them yourself following these directions: https://docs.ccr.buffalo.edu/en/latest/software/building/ You will want the ones available for the foss/2022a toolchain. If you run into issues, please submit a help ticket and we'll work with you to resolve the problem. We can certainly install this for you; however, there is a long wait time right now as we've got massive infrastructure work we're trying to complete before the semester starts.

[dmacguigan]

Hello Dori,

I will try using the Easy Build recipes for this software.

On another note, our lab has a considerable number of modules built using the old system (located in /projects/academic/tkrabben/modules_KrabLab/). Is there an easy way for us to switch these over to the new module system?

Best, Dan

-- Dan MacGuigan, PhD he-him-his NSF Postdoctoral Fellow Department of Biological Sciences University at Buffalo @DMacGuig

---

From: Dori Sajdak @.> Sent: Tuesday, August 1, 2023 9:36 AM To: ubccr/software-layer @.> Cc: Daniel Macguigan @.>; Mention @.> Subject: Re: [ubccr/software-layer] Software install request - RepeatModeler and RepeatMasker (Issue #56)

@dmacguiganhttps://github.com/dmacguigan it does not look like you're using CCR's new modules. Please see here for instructions: https://docs.ccr.buffalo.edu/en/latest/software/modules/ Since these are contained in the Easy Build recipe database, you can try building them yourself following these directions: https://docs.ccr.buffalo.edu/en/latest/software/building/ You will want the ones available for the foss/2022a toolchain. If you run into issues, please submit a help ticket and we'll work with you to resolve the problem. We can certainly install this for you; however, there is a long wait time right now as we've got massive infrastructure work we're trying to complete before the semester starts.

— Reply to this email directly, view it on GitHubhttps://github.com/ubccr/software-layer/issues/56#issuecomment-1660345747, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACC3FR7HARS4S4SRFDISRD3XTEA5NANCNFSM6AAAAAA26OSDR4. You are receiving this because you were mentioned.Message ID: @.***>

[dsajdak]

HI @dmacguigan did you still need these installed by CCR or did you get them installed yourself?

[dmacguigan]

Hello Dori,

I was unable to install this software. EasyBuild does not have a RepeatModeler recipe that is compatible with the cluster's compiler toolchains. And while RepeatMasker has a foss-2020b recipe, the software version is slightly out of date and I was unable to build it successfully anyway.

If you are able to install the latest versions of this software, I'm sure my lab and others would use them.

Best, Dan

-- Dan MacGuigan, PhD he-him-his NSF Postdoctoral Fellow Department of Biological Sciences University at Buffalo https://danjmac.weebly.com/ Google Scholarhttps://scholar.google.com/citations?user=ZfvNw2gAAAAJ&hl=en&authuser=1

---

From: Dori Sajdak @.> Sent: Wednesday, September 27, 2023 3:41 PM To: ubccr/software-layer @.> Cc: Daniel Macguigan @.>; Mention @.> Subject: Re: [ubccr/software-layer] RepeatModeler and RepeatMasker (Issue #56)

HI @dmacguiganhttps://github.com/dmacguigan did you still need these installed by CCR or did you get them installed yourself?

— Reply to this email directly, view it on GitHubhttps://github.com/ubccr/software-layer/issues/56#issuecomment-1737974168, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACC3FR3BCYTY757BOIGMHZLX4R6N5ANCNFSM6AAAAAA26OSDR4. You are receiving this because you were mentioned.Message ID: @.***>

[dsajdak]

@dmacguigan ok thanks for trying. We'll give it a try as well!

[dsajdak]

Hi @dmacguigan SUCCESS! RepeatModeler, RepeatMasker, and RepeatScout have been installed in the new software release. Use module spider repeat to find them and any dependencies

[dmacguigan]

Hi Dori,

That's great, thank you!

I see that you were able to build the latest versions of both software. Did you make custom easyconfig files? If so, would you mind sharing them? I'm trying to learn the new module system, so seeing working examples would be helpful.

Best, Dan

-- Dan MacGuigan, PhD he-him-his NSF Postdoctoral Fellow Department of Biological Sciences University at Buffalo https://danjmac.weebly.com/ Google Scholarhttps://scholar.google.com/citations?user=ZfvNw2gAAAAJ&hl=en&authuser=1

---

From: Dori Sajdak @.> Sent: Friday, September 29, 2023 4:48 PM To: ubccr/software-layer @.> Cc: Daniel Macguigan @.>; Mention @.> Subject: Re: [ubccr/software-layer] RepeatModeler and RepeatMasker (Issue #56)

Hi @dmacguiganhttps://github.com/dmacguigan SUCCESS! RepeatModeler, RepeatMasker, and RepeatScout have been installed in the new software release. Use module spider repeat to find them and any dependencies

— Reply to this email directly, view it on GitHubhttps://github.com/ubccr/software-layer/issues/56#issuecomment-1741472067, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACC3FR562VDQY77C4RAZH53X44X2ZANCNFSM6AAAAAA26OSDR4. You are receiving this because you were mentioned.Message ID: @.***>

[dsajdak]

Yes, I actually meant to share that with you. Some of them, I just had to change the GCC version from 11.3 to 11.2 but others needed some of the dependency versions changed and one had an issue with the sanity test passing. You can see my recipes here - #73