Suggested minor edits

[jlboat]

Hello,

I had some issues running the pipeline via the provided commands on an Ubuntu 20 VM. So, I went ahead and forked/fixed the problems I was having. I'm happy to put in a pull request, but I'm not sure if I've handled the changes in the way that you would prefer. That includes converting python2 scripts to 3 using 2to3 (plus some other minor edits), making a new folder for bash scripts (from slightly modified sbatch scripts), and deleting headers from some of the design files that were causing errors.

Let me know if you still want the pull request, and I'll put one in.

-Lucas

[lauren-mcintyre]

Lucas Have you seen the latest pipeline? Everything was converted I believe... there is a new paper look for "Testcross" first author Miller. Would be very bad if we have a deprecated link from your paper not directing to the newest code. Would also be bad if we still have v2 floating about Lauren

…

________________________________ From: J. Lucas Boatwright ***@***.***> Sent: Sunday, June 27, 2021 2:44 PM To: McIntyre-Lab/BayesASE ***@***.***> Cc: Subscribed ***@***.***> Subject: [McIntyre-Lab/BayesASE] Suggested minor edits (#1) [External Email] Hello, I had some issues running the pipeline via the provided commands on an Ubuntu 20 VM. So, I went ahead and forked/fixed the problems I was having. I'm happy to put in a pull request, but I'm not sure if I've handled the changes in the way that you would prefer. That includes converting python2 scripts to 3 using 2to3 (plus some other minor edits), making a new folder for bash scripts (from slightly modified sbatch scripts), and deleting headers from some of the design files that were causing errors. Let me know if you still want the pull request, and I'll put one in.

-Lucas — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_McIntyre-2DLab_BayesASE_issues_1&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=lnVATt_LlDyOygd8jM84Jw&m=HZvH8brj892Ht9pz2k0P32MwYUZIi9mPV7eFPOf9lu0&s=kXwpqk6vV_Zf4n4DRmUL0djZTTEO2eVauwCRQSf1nlI&e=>, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AE43DBOOK4SF5M47MGN6AV3TU5WR3ANCNFSM47MU6ELA&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=lnVATt_LlDyOygd8jM84Jw&m=HZvH8brj892Ht9pz2k0P32MwYUZIi9mPV7eFPOf9lu0&s=gPuBWjrgXycqyqPFlEsvldaQFfzmHnyPnHWEPAwgwUE&e=>.

[jlboat]

Hi Lauren!

I hope you're doing well. Yes, I saw this newly published pipeline and was excited about the changes you all made. I'm actually helping Doug/Pam write something on robust homoeolog-specific expression and suggested that we use this newer pipeline. I think all of the main code looks fine, I was just having minor trouble with the demo steps and thought I'd mention it. It may alternatively be an issue with my setup, but I thought I would check to make sure. Either way, I have it working on my system now. The available setup options (conda, Nextflow, etc) made getting everything running very easy.

Thanks for the quick reply.

[lauren-mcintyre]

Lucas Great. If you can send us what changes you needed to make it would be much appreciated Really good. To hear from you! Hope you are well Lauren

…

________________________________ From: J. Lucas Boatwright ***@***.***> Sent: Monday, June 28, 2021 9:38 AM To: McIntyre-Lab/BayesASE ***@***.***> Cc: McIntyre, Lauren M ***@***.***>; Comment ***@***.***> Subject: Re: [McIntyre-Lab/BayesASE] Suggested minor edits (#1) [External Email] Hi Lauren! I hope you're doing well. Yes, I saw this newly published pipeline and was excited about the changes you all made. I'm actually helping Doug/Pam write something on robust homoeolog-specific expression and suggested that we use this newer pipeline. I think all of the main code looks fine, I was just having minor trouble with the demo steps and thought I'd mention it. It may alternatively be an issue with my setup, but I thought I would check to make sure. Either way, I have it working on my system now. The available setup options (conda, Nextflow, etc) made getting everything running very easy. Thanks for the quick reply. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_McIntyre-2DLab_BayesASE_issues_1-23issuecomment-2D869693158&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=lnVATt_LlDyOygd8jM84Jw&m=73ve6RvdwwkkigFzudyJFybcj4Ym8QGI6Aw26qsP8vw&s=jroYCCSdGWpgOEFqkuXBhJtQ01_5HiLiNlJJoVbd2kc&e=>, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AE43DBPDDD6YYXWEQDXWUCTTVB3NRANCNFSM47MU6ELA&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=lnVATt_LlDyOygd8jM84Jw&m=73ve6RvdwwkkigFzudyJFybcj4Ym8QGI6Aw26qsP8vw&s=j_ABlHH_YwnBDSDSI3y10REDggNO48WrdA3tog7puHk&e=>.