Issuess with Scaffold files

[DianaBonillaEscobar]

Hello We are having issues using scaffold. After completing the clustering step, we get the usual message of "data processing is completed. However, neither the clustered.txt or the RData file are being created. We tried different datasets, different computers but no success yet. Any idea what could be wrong?

[pfgherardini]

Hi Diana,

Can you share a box folder with me with some sample data that is giving you problems?

Thanks

[pfgherardini]

Hi Diana,

Which version are using? The "master" branch or the "multiFilesClustering" branch?

[DianaBonillaEscobar]

Thanks Federico. The Master one D

Diana L. Bonilla, Ph.D., SCYM(ASCP)CM Senior Research Scientist Department of Immunology SCR3.2007 | 7455 Fannin Street, Houston, TX 77054 T 713 563 3229 F 713 563 3276

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From: Pier Federico Gherardini notifications@github.com Reply-To: nolanlab/scaffold reply@reply.github.com Date: Monday, July 2, 2018 at 3:39 PM To: nolanlab/scaffold scaffold@noreply.github.com Cc: "Bonilla Escobar,Diana L" DLBonilla@mdanderson.org, Author author@noreply.github.com Subject: Re: [nolanlab/scaffold] Issuess with Scaffold files (#10)

Hi Diana,

Which version are using? The "master" branch or the "multiFilesClustering" branch?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/nolanlab/scaffold/issues/10#issuecomment-401927643, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AmwpuwX2ZFYplU0y2f56AyahhQBv1kqCks5uCoUNgaJpZM4U6QbC. The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

[pfgherardini]

Hi Diana,

I am not sure what's going on things seem to work for me. Can you try installing it again (you only need to run the install_github portion)? Maybe you are using an older version.

Anyways, in a couple of weeks (definitely by July 26) I am going to release a totally revamped pipeline for doing scaffold analyses, which is going to have way less bugs, more documentation, and in general much better to use. If you can wait a couple of weeks, that's probably the easiest option.

[DianaBonillaEscobar]

Thanks Federico. I will try installing it again. Looking forward to using the scaffold pipeline, thank you so much for letting me know. Regards, Diana

Diana L. Bonilla, Ph.D., SCYM(ASCP)CM Senior Research Scientist Department of Immunology SCR3.2007 | 7455 Fannin Street, Houston, TX 77054 T 713 563 3229 F 713 563 3276

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From: Pier Federico Gherardini notifications@github.com Reply-To: nolanlab/scaffold reply@reply.github.com Date: Thursday, July 5, 2018 at 2:15 PM To: nolanlab/scaffold scaffold@noreply.github.com Cc: "Bonilla Escobar,Diana L" DLBonilla@mdanderson.org, Author author@noreply.github.com Subject: Re: [nolanlab/scaffold] Issuess with Scaffold files (#10)

Hi Diana,

I am not sure what's going on things seem to work for me. Can you try installing it again (you only need to run the install_github portion)? Maybe you are using an older version.

Anyways, in a couple of weeks (definitely by July 26) I am going to release a totally revamped pipeline for doing scaffold analyses, which is going to have way less bugs, more documentation, and in general much better to use. If you can wait a couple of weeks, that's probably the easiest option.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/nolanlab/scaffold/issues/10#issuecomment-402825202, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AmwpuwHFugmP7PCT1HPgJM9Msvx8eDloks5uDmW_gaJpZM4U6QbC. The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.