Add HTML version of Tom's tutorials.

Tutorials/genome_groups.html

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+<h1>
+How to create and access genome groups
+</h1>
+
+Creating a genome group in your workspace allows you to create logical
+groups of genomes for downstream comparative analysis. In this
+example, you will create two genome groups. One genome group will
+contain only Streptococcus aureus, and the second genome group will
+contain all Streptococcus genomes except those from Streptococcus
+aureus.
+<p>
+
+This example assumes familiarity with a few other commands in the CLI
+to create the input file containing the genomes to be put in the new
+genome group. You do not need to be familiar with these commands, just
+the format of the input file. The format of the input file is simply a
+list of genome ids, one per line with no other information in the
+file.
+<p>
+<pre>
+$ p3-all-genomes --in genome_name,aureus > Staphylococcus.aureus.genomes
+$ p3-all-genomes --in genome_name,Staphylococcus > Staphylococcus.all.genomes
+$ a_not_b Staphylococcus.all.genomes Staphylococcus.aureus.genomes > Staphylococcus.not.aureus.genomes
+
+$ wc *.genomes
+    9257   41089  399759 Staphylococcus.all.genomes
+    8383   36955  356756 Staphylococcus.aureus.genomes
+     876    4146   43099 Staphylococcus.not.aureus.genomes
+   18516   82190  799614 total
+</pre>
+<p>
+Let's take a quick look at a few entries in each file using the unix
+head command. In this case, the first five lines of each file are
+displayed. Notice that the header exists in two of the three files. It
+is not in the file created with the a_not_b command because the header
+appeared in both input files to the a_not_b command.
+<p>
+<pre>
+$ head -n 5 *.genomes
+==> Staphylococcus.all.genomes <==
+genome.genome_id
+904758.3
+904731.3
+904739.3
+904750.3
+
+==> Staphylococcus.aureus.genomes <==
+genome.genome_id
+904758.3
+904731.3
+904739.3
+904750.3
+
+==> Staphylococcus.not.aureus.genomes <==
+1000590.6
+1008454.3
+1034809.4
+1078083.3
+1115805.3
+</pre>
+
+<p>
+
+The input files to create genome groups are almost ready. The input to
+p3-put-genome-group is a single column file with the only values being
+genome ids. The header needs to be removed. We can easily do this with
+an editor, or use the unix grep command with the -v option. For this
+example, we will just edit the file with an editor and remove the
+header.
+<p>
+The p3-put-genome-group takes the list of genome ids on standard
+input. Using the unix cat command we can send the contents of our
+newly created files of genome ids to the p3-put-genome-group command
+with the following command.
+<p>
+<pre>
+$ cat Staphylococcus.not.aureus.genomes | p3-put-genome-group "Staphlococcus not aureus"
+$ cat Staphylococcus.aureus.genomes | p3-put-genome-group "Staphylococcus aureus"
+</pre>
+<p>
+
+The two newly created genome groups are now visible and usable in your
+workspace using on the PATRIC web site, as well as accessible using
+the command line interface.
+
+<pre>
+$ p3-get-genome-group "Staphylococcus aureus"
+904758.3
+904731.3
+904739.3
+904750.3
+904763.3
+904725.3
+904734.3
+904737.3
+904754.3
+904768.3
+&lt;...>
+</pre>
+

Tutorials/logging_in.html

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+<h1>Logging in</h1>
+
+For operations on private data, such as that data stored in your
+workspace, you will need to be logged in. You can check to see if you
+are already logged in using the p3-whoami command:
+
+<pre>
+$ p3-whoami
+You are logged in as:
+[email protected]
+</pre>
+
+<p>
+If you were not logged in, when you run the p3-whoami command you
+would see that you are not logged in. If this were the case, you would
+not be able to upload to your workspace or see any of the data in your
+workspace for example.
+<p>
+<pre>
+$ p3-whoami
+You are not logged in.
+</pre>
+
+<p>
+
+If you are not logged in, you can do so using the p3-login
+command. Notice that your user name contains the suffix
+“@patricbrc.org”. This suffix is required so that your PATRIC
+credentials are used rather than your RAST credentials. 
+
+<pre>
+$ p3-login [email protected]
+Password: ****
+Logged in with username [email protected]
+$ p3-whoami
+You are logged in as:
+[email protected]
+</pre>

Tutorials/uploading_data.html

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+<h1>
+Uploading data from the command line into your workspace
+</h1>
+
+The PATRIC workspace is a place where you can upload your data so that
+it can be integrated with existing public data in PATRIC while at the
+same time maintaining privacy. As an example, you can upload contigs
+to your workspace, annotate them using the PATRIC annotation service,
+and then compare the annotated results with publicly annotated genomes
+in PATRIC.
+<p>
+
+In this example, I am going to upload contigs from my mac to my
+workspace in PATRIC using the command line interface rather than using
+the web interface for uploading contigs to my workspace.
+<p>
+<h2>Uploading data</h2>
+
+The ws-create command is used to upload data to my workspace:
+
+<pre>
+$ ws-create -h
+ws-create.pl [-ahopu] [long options...] <name> <type> <filename>
+	     -p --permission   Permissions for folders created
+	     -u --useshock     Upload file to shock and store link in workspace
+	     -o --overwrite    Overwrite existing destination object
+	     --wsurl           Workspace URL
+	     -a --admin        Run as administrator
+	     -h --help         Show this usage message
+$ ws-create -u /[email protected]/home/MinhashDev/UC.MICU.02.30.fastq Reads /home/brettin/assemblies/UC.MICU.02.30.fastq
+</pre>
+<p>
+
+In this case, I used the -u option to tell the system to upload the genomes into the Shock bulk
+storage system; for any file larger than a few kilobytes we recommend that this option be used.
+<p>
+If I want to verify the uploaded reads, I can use do a listing on
+the folder that I uploaded the reads to.
+<p>
+<pre>
+$ ws-ls /[email protected]/home/MinhashDev
+
+Name                Owner                 Type       Moddate             Size       User perm Global perm
+UC.MICU.02.30.msh   [email protected] job_result 2016-10-01T03:04:01       1513 o         n          
+.UC.MICU.02.30.msh  [email protected] folder     2016-10-01T01:19:34          0 o         n          
+UC.MICU.02.30.fastq [email protected] reads      2016-09-30T21:34:12 8284314281 o         n    
+</pre>
+
+<p>
+
+The folder listing includes fields such as owner, the object's name
+(specified by first positional argument in the ws-create command) type
+(specified by the second positional argument) and permissions
+(specified by the third positional argument).
+