diff --git a/qiita_pet/support_files/doc/source/faq.rst b/qiita_pet/support_files/doc/source/faq.rst index 7291467b2..3e5ce1834 100755 --- a/qiita_pet/support_files/doc/source/faq.rst +++ b/qiita_pet/support_files/doc/source/faq.rst @@ -244,6 +244,90 @@ etc; for more information check `this 3 minute read about 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? ------------------