setup, cont

Author: bluegenes

.gitignore

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+*.py[co]
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+
+#Translations
+*.mo
+
+#Mr Developer
+.mr.developer.cfg
+
+_build
+*~
+
+html

assembly-evaluation.md

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+#Placeholder for assembly evalutation tutorial

code-of-conduct.rst

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+Workshop Code of Conduct
+========================
+
+All attendees, speakers, sponsors and volunteers at our workshop
+are required to agree with the following code of conduct. Organisers
+will enforce this code throughout the event. We are expecting
+cooperation from all participants to help ensuring a safe environment
+for everybody.
+
+**tl; dr: be excellent to each other.**
+
+Need Help?
+----------
+
+You can reach the course director, Titus Brown, at [email protected]
+or via the cell phone number he has sent out.  You can also talk to
+any of the instructors or TAs if you need immediate help, or (in an
+emergency) call 911.
+
+Sue McClatchy, [email protected] is the person to contact if
+Titus is not available or there are larger problems; she is readily
+available by e-mail.
+
+The Quick Version
+-----------------
+
+Our workshop is dedicated to providing a harassment-free workshop
+experience for everyone, regardless of gender, age, sexual
+orientation, disability, physical appearance, body size, race, or
+religion (or lack thereof). We do not tolerate harassment of workshop
+participants in any form. Sexual language and imagery is not
+appropriate for any workshop venue, including talks, workshops,
+parties, Twitter and other online media. Workshop participants
+violating these rules may be sanctioned or expelled from the workshop
+*without a refund* at the discretion of the workshop
+organisers.
+
+The Less Quick Version
+----------------------
+
+Harassment includes offensive verbal comments related to gender, age,
+sexual orientation, disability, physical appearance, body size, race,
+religion, sexual images in public spaces, deliberate intimidation,
+stalking, following, harassing photography or recording, sustained
+disruption of talks or other events, inappropriate physical contact,
+and unwelcome sexual attention.
+
+Participants asked to stop any harassing behavior are expected to
+comply immediately.
+
+If a participant engages in harassing behavior, the workshop
+organisers may take any action they deem appropriate, including
+warning the offender or expulsion from the workshop with no refund.
+
+If you are being harassed, notice that someone else is being harassed,
+or have any other concerns, please contact a member of workshop
+staff immediately.
+
+Workshop instructors and TAs will be happy to help participants
+contact KBS security or local law enforcement, provide escorts, or
+otherwise assist those experiencing harassment to feel safe for the
+duration of the workshop. We value your attendance.
+
+We expect participants to follow these rules at workshop and workshop
+venues and workshop-related social events.
+
+This work is licensed under a `Creative Commons Attribution 3.0
+Unported License <http://confcodeofconduct.com/>`__.
+
+----
+
+This Code of Conduct taken from http://confcodeofconduct.com/. See
+
+http://www.ashedryden.com/blog/codes-of-conduct-101-faq
+
+for more information on codes of conduct.

filezila-file-transfer.md

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+# Downloading and Transferring Files
+
+Our goals for this lesson are:
+
+* Download a file from the internet with wget
+* Transfer a file from a remote machine to your computer with FileZilla
+* Transfer a file from your computer to a remote machine with FileZilla
+* Name other tools that can be used for file transfer
+
+## Download file from the internet to your remote machine
+
+One way to download files to your remote instance from a webserver is to use the command line tool, *wget*. This command supports downloading files from FTP and HTTP(s). The tool *wget* also supports recursive download (with the parameter *-r*), allowing you to download content from a directory or folder. For your information, there are other command line tools that can also be used to download data (e.g., *curl*), but *wget* should serve you well for this lesson and bioinformatic analysis.
+
+An example of this would be: 
+```bash
+$ cd ~
+$ wget https://static.pexels.com/photos/104827/cat-pet-animal-domestic-104827.jpeg 
+```
+
+And now, you will have a file named `cat-pet-animal-domestic-104827.jpeg` on your remote instance in our home directory. 
+
+Now we have a conundrum! We have downloaded a file that we know is a cat photo, but we can't view it on our remote machine! Let's use FileZilla to facilitate the transfer so we can take a look.
+
+## Transfer Files From Your Instance with Filezilla
+Let's pretend that we didn't just grab that cat photo from the internet, and we have something unique that we would like to view. For this, *wget* would not work. Instead, you can use FileZilla to transfer a file from your local machine to a remote instance, or vice versa. 
+
+### Open the site manager
+
+Open *FileZilla*, and click on the File tab. Choose 'Site Manager'.
+ 
+![FileZilla_step1](_static/filezilla_1.png)
+
+### Get The Key File
+
+See the instructions under ["Getting your private key"](jetstream/login.html#getting-the-private-key) to download your key file. This will allow you to authenticate
+with your instance. Please do not post this file publicly!
+
+### Add your instances as a site
+
+Within the 'Site Manager' window, do the following: 
+
+1. Click on 'New Site', and name it something intuitive (e.g. ANGUS or jetstream_angus)
+2. Host: address of your cloud instance. Should be of the form W.X.Y.Z.
+3. Protocol: SFTP - SSH File Transfer Protocol
+4. Logon Type: Key file
+5. User: `tx160085`
+6. Keyfile: The key you downloaded.
+7. Click 'Connect'
+	
+![FileZilla_step2](_static/filezilla_site_add.png)
+
+### Filezilla - Step 3
+
+In FileZilla, on the left side of the screen navigate to the location you would like to save the file, and on the right side of the screen navigate through your remote directory to the file `~/cat-pet-animal-domestic-104827.jpeg`. Double click on the .jpeg file to transfer a copy, or click and drag over to the right hand panel.
+
+Open the file on your local machine, and bask in the glory of the cute cat.
+
+We could also use `scp` or `rsync` to transfer files. These are command line utilities. If you're transferring a large datafile, `rsync` may be slightly better, because if the download fails it will restart from where it left off. 
++ [rsync](https://rsync.samba.org/)
++ scp

toc.rst

@@ -10,46 +10,31 @@ Table of Contents
 
    jetstream/boot
    jetstream/login
-   filezila-file-transfer
 
-   running-command-line-blast
-   running-blast-large-scale
-   visualizing-blast-scores-with-RStudio
    command-line-and-rstudio
 
    quality-trimming
-   variant-calling
+   assembly-trinity
+
+   assembly-evaluation
+   dammit_annotation
 
-   introduction-to-R-and-dataframes
    counting
+   deseq2-asthma
 
-   genome-assembly
-   prokka_genome_annotation
+   rmarkdown_rnaseq
+   
+   kmers-and-sourmash
 
    introduction-to-automation
 
-   kmers-and-sourmash
-   
-   rmarkdown_rnaseq
-
-   GATK_pipeline
-   GWAS
-   meta_GWAS
 
    Jupyter-Notebook-Notes
    github
-   fotis-jupyter
    database_resources
+   filezila-file-transfer
 
    analyzing_nanopore_data
 
-   rmarkdown_rnaseq
-
-   deseq2-asthma
-   chip-seq
-   
-   assembly-trinity
-
-   dammit_annotation
 
    for-instructors/index