Merge pull request #3052 from antgonza/fix-3051

Fix 3051

Author: adswafford

qiita_pet/support_files/doc/source/faq.rst

@@ -244,6 +244,90 @@ etc; for more information check
 `this 3 minute read about Markdown <https://guides.github.com/features/mastering-markdown/>`__.
 
 
+I want to transfer a lot of files to Qiita, is there an easy way?
+-----------------------------------------------------------------
+
+Yes! This is available in the "Upload Files" section of each study by accessing the tab
+"Upload via Remote Server (ADVANCED)".
+
+We currently suggest using scp, note that your server where you store your files should allow
+connecting to it via scp - in other words, this only works when moving files from a server to Qiita.
+
+Now, the way it works is that you need to create a new secure key to that server, imagine
+that you are making a copy of your storage-shed key, then you share that key to Qiita (you will give
+access to Qiita to run a single copy command in your server), Qiita uses that key and securely
+destroy it.
+
+To take advantage of this feature you need to:
+
+#. Prepare all the files you want to transfer in a single folder (or you can transfer
+   multiple times from multiple folders into one study). Note that Qiita will only collect
+   files with valid extensions from the top level directory (no sub-directories); see the
+   top of the "Upload Files" page within your study for the latests list of valid extensions.
+#. In your server (this needs to be run within your home directory in the server where you
+   store the files!), generate a new key by running:
+   `ssh-keygen -t rsa -C "ssh test key" -f ~/.ssh/qiita-key -P ""`. Here is where you are
+   creating that key to your storage-shed.
+#. Allow access using the new key to new connections (this also needs to be run in the
+   remote server): `cat ~/.ssh/qiita-key.pub >> ~/.ssh/authorized_keys`. This tells the
+   server that is OK to give access to the key created to your storage-shed; note that if
+   you want to completely stop that key to work you can open that file and remove the line
+   with the name of this key.
+#. Dowload your new generated key `qiita-key` (the file) to your local computer and use it
+   in the `Key` option of "Upload via Remote Server (ADVANCED)".
+
+Using this key you can `List Files` to test the connection and verify the list of study files. Then,
+if the connection is made and files are correct, press 'Transfer Files' to initiate the transfer.
+
+Note that if you click multiple times, too quickly there is a chance that your server will block
+Qiita, if this happens, just wait a few minutes and retry again.
+
+
+How do I update the sample or preparation file?
+-----------------------------------------------
+
+Remember, these are separate files so they need to be updated separately. In both cases,
+the easiest is to upload the new file from your computer to Qiita using the `Upload Files`
+button in your study. Once the file you want to use is there you can use them within Qiita.
+
+To update a sample information file: Click on `Sample Information` button in the your study
+page, then use the `Update sample information` section on that page to select your file and
+update it. Note that for this you can also directly upload your file via the
+`Direct upload file (< 2MB)`.
+
+To update a preparation information file: Click on the preparation you want to update within
+your study page, then click on `Summary`, and use the `Update prep information` section on
+that page to select your file and update it.
+
+Note that these information is generally independent of the sequence processing so you
+don't need to reprocess your sequences; however, if you use your study in an analysis, you will
+need to recreate that analysis to use the updated sample or preparation metadata
+
+
+When do I need the run_prefix in my preparation information file?
+-----------------------------------------------------------------
+
+It depends on your sequence processing but in general it will facilitate loading your
+files to your preparation in Qiita.
+
+First of all, this is a prefix value so you only need the beginning of the file
+name to load the files in Qiita; for example if your file names for a given sample are:
+AWERWADFA_I1.fastq.gz, AWERWADFA_R1.fastq.gz, AWERWADFA_R2.fastq.gz, the run_prefix for
+the sample should be AWERWADFA. Qiita will use that to group those files under the same
+sample with that run_prefix.
+
+Now the run_prefix is used constantly within file selection and processing in all file types but
+specially on:
+
+- BIOM: the run_prefix is used to rename the samples in your BIOM to match the sample names
+  in Qiita. Basically, if you add the sample names in your BIOM file as the run_prefix and the
+  sample name in Qiita in the sample_name column of your preparation, Qiita will automatically
+  rename them to match.
+- per sample FASTQ: run_prefix is the way to link which sample goes with which files so using here
+  will facilitate loading your files to the preparation and then used for processing, without it
+  Qiita will not be able to process your samples.
+
+
 How to cite Qiita?
 ------------------