General Information
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Contact: Please email hbctraining@hsph.harvard.edu for more information. For any Orchestra-specific questions, please email rchelp@hms.harvard.edu.
Etherpad: https://etherpad.net/p/HBC_intro_to_unix
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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Schedule
| ********************************* Day1 (October 8th) Schedule ********************************* | ||
|---|---|---|
| 9:00 - 9:30 | Welcome , introductions, code of conductand Introductions | All |
9:30 - 9:50 | Introduction to workshop, scope, learning objectives | Radhika |
| 9:50 - 10:30 | Unix 1: Introduction to the shell | Radhika |
10:30 - 10:45 | Coffee | |
| 10:45 - 11:35 | Unix 1: Introduction to the shell (continued) | Radhika |
| 11:35 - 12:30 | Unix 2: Searching and redirection | Mary |
12:30 - 13:30 | Lunch | |
| 13:30 - 14:30 | Unix 3: For "for" loop and shell scripts | Meeta |
14:30 - 15:00 | Radhika | |
15:00 - 15:15 | Coffee | |
15:15 - 15:45 | Radhika | |
| 15:45 - 17:00 | Introduction to Orchestra basics | Kris Holton, HMS-RC |
| ********************************* Day2 (October 9th) Schedule ********************************* | ||
|---|---|---|
| 9:00 - 9:10 | HPC refresher | Radhika |
9:10 - 9:40 | Meeta | |
| 9:40 - 10:30 | Data QC | Mary |
10:30 - 10:45 | Coffee | |
| 10:45 - 11:25 | Data QC (continued) | Mary |
| 11:25 - 12:30 | RNA-Seq workflow | Radhika Meeta |
12:30 - 13:30 | Lunch | |
| 13:30 - 14:00 | RNA-Seq workflow (continued) | Radhika Meeta |
14:00 - 15:00 | MeetaRadhika | |
15:00 - 15:15 | Coffee | |
15:15 - 16:15 | MeetaRadhika | |
| 15:45 - 17:00 | Resources and wrap-up | Radhika |
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To participate in this workshop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) before the start of your workshop. Participants are strongly encouraged to bring and use their own laptops to insure ensure the proper setup of tools for an efficient workflow once you leave the workshop.
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a) install the following programs
Mac users
1. Java
2. Filezilla
3. Integrative Genomics Viewer (IGV)
34. Text Wrangler or Sublime Text
Windows users
1. Putty
2. Java
3. Filezilla
4. Integrative Genomics Viewer (IGV)
35. Notepad++
If you would like us to check your installations prior to class, please arrive at 8:30am on Thursday, and email us any questions about the installations.
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This workshop was sponsored by the HMS Tools and Technology Committee (TnT) and the Harvard NeuroDiscovery Center (HNDC).
The structure, objectives, and workflow of this workshop is derived from the Data Carpentry genomics workshop. Data Carpentry is supported by the Gordon and Betty Moore Foundation and a partnership of several NSF-funded BIO Centers (NESCent, iPlant, iDigBio, BEACON and SESYNC) and Software Carpentry. The structure and objectives of the curriculum as well as the teaching style are informed by Software Carpentry.
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