FTP Download Made Easy: A Step-by-Step Tutorial
Please do not download CD or DVD images with your web browser the wayyou download other files! The reason is that if your downloadaborts, most browsers do not allow you to resume from the point where itfailed.
Instead, please use a tool that supports resuming - typicallydescribed as a download manager. There are many browser pluginsthat do this job, or you might want to install a separateprogram. Under Linux/Unix, you can use aria2, wxDownload Fast or (on thecommand line) wget -c URL orcurl -C - -L -O URL. Thereare many more options listed in a comparisonof download managers.
The first CD/DVD disk contains all the files necessaryto install a standard Debian system.To avoid needless downloads, please do not downloadother CD or DVD image files unless you know that you need packages onthem.
Links to experiment family downloads in various formats and supplementary files are provided at the foot of each GEO Series record. These files are compressed using gzip (.gz or .tgz extension). To unzip and read these files, please use a utility such as WinZip or 7-Zip.
All GEO records and raw data files are freely available for bulk download from our FTP site. Please see our README for details on directory structure and file formats. However, GEO now holds such large numbers of submissions that some parent directories can no longer be accessed using web browsers due to time-out errors. In such cases it is necessary to bypass the parent directory and go directly to the target directory, e.g. for Series GSE1000:
The Accession Display bar is found at the top of each GEO record and can be used to download or view complete or partial records, or related Platform, Sample and Series records. The Scope feature allows display of a single accession number (Self) or any (Platform, Sample, or Series) or all (Family) records related to that accession. Amount dictates the quantity of data displayed, with choices including metadata only (Brief), metadata and the first 20 rows of the data table (Quick), data table only (Data), or full metadata/data table records (Full). Format controls whether records are displayed in HTML, SOFT (plain text) or MINiML (XML) format.
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Links to DataSet SOFT files are available under the 'download' button on each DataSet record. These files are compressed using gzip (.gz or .tgz extension). To unzip and read these files, please use a utility such as WinZip or 7-Zip.
All GEO DataSet records are freely available for bulk download from our FTP site. These files are compressed using gzip (.gz extension). To unzip and read these files, please use a utility such as WinZip or 7-Zip. Alternatively, if you have UNIX, use the gunzip command to uncompress the files, e.g.,
If you only are interested in the metadata and text of an article or author manuscript, then bulk download may be what you want to use. Bulk packages group together hundreds of thousands of articles in XML or plain text formats in compressed packages (Note: The Historical OCR Dataset is only available in plain text format). If you are also interested in media files, supplementary materials, or PDFs, please see the sections on Individual Article Download and PDF Download.
If you only want to download some of the PMC OA Subset based on search criteria or if you want to download complete packages for articles that include XML, PDF, media, and supplementary materials, you will need to use the individual article download packages. To keep directories from getting too large, the packages have been randomly distributed into a two-level-deep directory structure. You can use the file lists in CSV or txt format to search for the location of specific files or you can use the OA Web Service API. The file lists and OA Web Service API also provide basic article metadata.
The ENA File Downloader is a new Java based command line application that you can downloadfrom GitHub.You can submit one or more comma separated accessions, or a file with accessions that youwant to download data for. This tool allows downloading of read and analysis files,using FTP or Aspera. It has an easy to use interactive interface and can also createa script which can be run programatically or integrated with pipelines.
The ENA FTP Downloader is a Java GUI application you can download fromGitHub.Given an accession, this program will present a list of associated read or analysis files youcan download.Alternatively, you can provide a file report generated from our Advanced Search API (ENA PortalAPI) to perform a bulk download of all files for a given set of criteria.Learn more about these APIs from our guide on How to Access ENAProgrammatically.
enaBrowserTools is a set of Python-based utilities which can be found here.These are simple-to-run scripts which allow accession-based data downloadcommands with the option to create more complex commands.Read more about this page in the enaBrowserTools Guide.
Aspera ascp command line client can be downloaded from Aspera.Please select the correct version for your operating system.The ascp command line client is distributed as part of the Aspera connecthigh-performance transfer browser plug-in.
Sometimes you may experience slowness or incomplete files when downloading from our FTP servers due to high load or ongoing maintenance. If the issue persists, please report it at here .You could also use other download methods such as Aspera or Globus, which might provide better performance than FTP.
Most modern web browsers no longer support the FTP protocol. For this reason, on the ENA Browser links to files hosted on FTP are internally converted to http when clicked for enabling downloads. You can copy the download links from ENA Browser and use them with non-browser clients (like wget or curl). If you still want to download using a web browser then please replace ftp:// with http:// in the URL.e.g. _1.fastq.gz -> _1.fastq.gz
To obtain a file's location (URL) to use with rsync (rsync://hgdownload.soe.ucsc.edu/... orrsync://hgdownload-euro.soe.ucsc.edu/...), navigate in your browser to our FTP site at or our downloads page at , and look for your file of interest. To learn more about rsync's options, type "man rsync" on the command line.
However, downloading via your browser will be very slow or may even time out for large files (i.e., bigBed, bigWig, BAM, VCF, etc.). Also, Safari does not support FTP inside the browser. When you enter a FTP URL in Safari, you may have to select "Guest" and click submit to log in before a FTP file system will open in a window on your desktop.
We do not encourage the use of FTP for downloading large data files. Rsync is a more efficient and convenient transport mechanism, and is therefore quicker and easier touse for downloading our data files. However, here are the command line steps for FTP, should you choose to use it:
To download multiple files from the UNIX ftp command line, use the "mget" command. You maywant to use the prompt command to toggle the interactive mode if you do not want to beprompted for each file that you download.
The Crustal Dynamics Data Information System (CDDIS) supports data archiving and distribution activities for a global user community. Since its inception, users have relied on anonymous ftp for accessing and downloading files from the system. Although this protocol allows users to easily automate file downloads, many organizations, data systems, and users have already migrated from ftp or are actively pursuing a move away from the protocol due to problems from a system and security standpoint. U.S. Government agencies have become increasingly concerned about this legacy protocol and ensuring data integrity for the user community and have disallowed the use of the ftp protocol. The CDDIS, located at NASA GSFC, has therefore addressed these concerns and provided alternative methods for access to its archive for continued easy and automated download of its contents.
There are 3 steps to complete before receiving the file:Download the apache commons net jar file (commons-net-3.6.jar) from: -net/download_net.cgi.
Save the code below to a file.
Compile and run the code.
Step 2 is below and Step 3 is shown after the code.
When FTP is transferring over the data connection, the control connection is idle. If the transfer takes too long, the firewall or NAT may decide that the control connection is dead and stop tracking it, effectively breaking the connection and confusing the download. The single HTTP connection is only idle between requests and it is normal and expected for such connections to be dropped after a time-out.
Most common download managers can receive files hosted on FTP servers, while some of them also give the interface to retrieve the files hosted on FTP servers. DownloadStudio allows not only download a file from FTP server but also view the list of files on a FTP server.
Simple File Transfer Protocol (the first protocol abbreviated SFTP), as defined by RFC 913, was proposed as an (unsecured) file transfer protocol with a level of complexity intermediate between TFTP and FTP. It was never widely accepted on the Internet, and is now assigned Historic status by the IETF. It runs through port 115, and often receives the initialism of SFTP. It has a command set of 11 commands and support three types of data transmission: ASCII, binary and continuous. For systems with a word size that is a multiple of 8 bits, the implementation of binary and continuous is the same. The protocol also supports login with user ID and password, hierarchical folders and file management (including rename, delete, upload, download, download with overwrite, and download with append).