Ibm Box File Upload From Unix Server

SRA File Upload

File Transfer Protocol (FTP)

In order to upload your files to the NCBI server via FTP you need the following information:

• Address
• Username
• Countersign

Effigy 1: Credentials for file uploading in the Submission Portal

FTP Command Line Basics

File transfer tin exist initiated in Windows Command Prompt (Get-go -> Control Prompt), Mac Last (Finder -> Applications -> Utilities -> Terminal), Linux, and Unix.

Activity	Command line
Change into directory with your information files	cd "U:\SRA\example-files"
Invoke FTP protocol	ftp -i
Access NCBI FTP server	open ftp-individual.ncbi.nlm.nih.gov
Provide username on "User" prompt	Username
Provide countersign on "Password" prompt	Countersign
Create directory	mkdir MYSUBMISSION
Change into that directory with arbitrary name	cd MYSUBMISSION
Transfer all files	mput *

Useful FTP commands:

Command	Information
assist, ?	Either command prints list of commands
!	Toggles back and forth betwixt the operating system and ftp. Once back in the operating system, blazon 'exit' to get back to the FTP command line.
bye, quit	These commands cease the FTP session and exit
ls	Lists files in the remote directory
put	Send one file

FTP Control line Instructions for the SRA Submission Portal Wizard

After you lot connected to the NCBI FTP server:

1. Navigate (use command cd) to your account folder uploads/user@email.com_xxxxx

2. Create a submission folder (use command mkdir) for your information inside your FTP account binder (uploads/user@email.com_xxxxx) and deposit your files into the submission folder. If you upload your files in the account folder directly or place the files into a nested folder, you lot volition not be able to meet or select the submission folder as instructed below. The submission folder is a temporary property area and it will be removed later the whole submission is finished processing (the button Submit is clicked).

Using tertiary party FTP clients

Many reliable FTP clients tin exist plant on Internet. For example, Filezilla and NcFTP Client are free for download. Please refer to their documentation for usage instructions and troubleshooting tips.

Using FileZilla to transfer files when making submission in the SRA Submission Portal Wizard

When using FileZilla to upload files y'all demand to paste your account folder'southward proper noun into the Remote Site box on the correct manus side of FileZilla interface (outlined in red) and striking Enter. Until you lot do this, you volition run into a message stating " 550 /: Permission denied " or " Neglect to read the directory listing ". We forbid directory listing in the default sign in folder for security reasons. From within your business relationship folder you tin can then create your submission binder(southward) for your submission(s).

Figure 2

Aspera Connect

Aspera Connect is software that allows download and upload via a web plugin for pop browsers on machines running Linux, Windows, and Macintosh. The software likewise includes a command line tool (ascp) that allows scripted data transfer. The software client is complimentary for users exchanging data with NCBI.

Aspera Connect Fast and Secure Protocol (FASP) uses User Datagram Protocol (UDP) that eliminates and overcomes many shortcomings of other FTP clients and we recommend it for all medium to large submissions and irksome or unreliable connections (especially from abroad).

Download and install Aspera Connect software from: http://downloads.asperasoft.com/en/downloads/8?list .

Aspera command line for the SRA Submission Portal Wizard

You lot may apply the following command to upload files via Aspera control line:

<path to aspera executables> -i <path/to/primal-file> -QT -l 100m -k1 -d <path/to/folder-with-file(s)> subasp@upload.ncbi.nlm.nih.gov:uploads/<user@email.com_xxxxx>

Aspera command line explanation:

• <user@email.com_xxxxx> is your personal account SRA folder generated for you and is listed under the Aspera Command-Line upload link;
• <path to aspera executables> or in many cases, simply, ascp:
  • Microsoft Windows: C:\Program Files\Aspera\Aspera Connect\bin\ascp.exe
  • Mac OS Ten: /Applications/Aspera/Connect.app/Contents/Resources/ascp (for admin's installation) or /Users/[username]/Applications/Aspera/Connect.app/Contents/Resource/ascp (for non-admin's installation)
  • Linux: /opt/aspera/bin/ascpor /home/[username]/aspera/connect/bin/ascp
• i <path/to/key_file> - accented path and file proper name of the private SSH key (e.chiliad.: /home/keys/aspera.openssh)
• <central-file> is provided upon your clicking on Get the key file link or sent upon request for direct SRA uploads
• Q - for adaptive period control (needed for disk throttling)
• T - to disable encryption
• k1 - enables resuming of partial transfers
• d - <path/to/folder-with-file(s)> should include a directory name and so should not be '.' Or './'
• l100m - designates maximum bandwidth of 100Mps, endeavor 100m and move up if necessary to ensure good performance with unattended operations
• <path/to/folder-with-file(south)> - names of files to transfer including path or path to a folder that contains all files

The ecology variable ASPERA_SCP_PASS can be used to store the private key path for a scripted series of majority uploads.

Aspera Connect Download .

A submission folder <binder-with-file(southward)> volition exist created automatically by Aspera within your account folder <user@email.com_xxxxx> when the option -d is provided.

At the last step of your submission, the submission folder containing your files can exist selected and the files will link to your submission.

Do non upload complex directory structures and files that practise not contain sequence data!

The submission folder is a temporary holding expanse and it volition be removed after the whole submission is finished processing (the push Submit is clicked).

Firewall Requirements

UDP (User Datagram Protocol for Aspera Connect) transfer must be enabled for the following IP ranges (delight consult your local network admin if yous are unsure): 130.xiv.29.0/24 and 130.xiv.250.0/24. TCP (Transmission Control Protocol for FTP) port 22 and UDP port 33001 must be open for our subnet.

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Email sra@ncbi.nlm.nih.gov for help.

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Source: https://www.ncbi.nlm.nih.gov/sra/docs/submitfiles

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