ae5fe3be649000cb4c68fe6bcf9401b8f8776baf jnavarr5 Fri May 3 16:02:33 2019 -0700 Adding rsync and FTP examples for hgdownload-euro, refs #20551 diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index 1bbf031..bbc578c 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -1215,58 +1215,67 @@ the Downloads page. If the desired conversion file is not listed, send a request to the genome mailing list and we may be able to generate one for you.

Downloading genome data

Most of the underlying tables containing the genomic sequence and annotation data displayed in the Genome Browser can be downloaded. All of the tables are freely usable for any purpose except as indicated in the README.txt file in the download directories. This data was contributed by many researchers, as listed on the Genome Browser Credits page. Please acknowledge the contributor(s) of the data you use.

Downloading the data

-Genome data can be downloaded in different ways:

+Genome data can be downloaded in different ways using our North American and European download +servers, hgdownload and hgdownload-euro.

Via rsync:
- The UCSC Genome Browser hgdownload server contains download - directories for all genome versions currently accessible in the Genome Browser. The rsync command - rsync -a -P rsync://hgdownload.soe.ucsc.edu/path/file ./ can quickly and efficiently - download large files to your current directory (./). To download an entire directory (note the - trailing slash), you would use an expression such as - rsync -a -P rsync://hgdownload.soe.ucsc.edu/directory/ ./ For more information please - click here.
+ The UCSC Genome Browser hgdownload server contains download directories for all genome versions + currently accessible in the Genome Browser. Either of the following rsync commands can quickly + and efficiently download large files to your current directory (./). + 
rsync -a -P rsync://hgdownload.soe.ucsc.edu/path/file ./
+ 
rsync -a -P rsync://hgdownload-euro.soe.ucsc.edu/path/file ./
+
+ To download an entire directory (note the trailing slash), you would use an expression such + as:
+ 
rsync -a -P rsync://hgdownload.soe.ucsc.edu/directory/ ./
+ 
rsync -a -P rsync://hgdownload-euro.soe.ucsc.edu/directory/ ./
+
+ For more information please click here.
Via ftp:
- The UCSC Genome Browser ftp server contains download directories - for all genome versions currently accessible in the Genome Browser. The ftp command - ftp://hgdownload.soe.ucsc.edu/goldenPath/ will take you to a directory that contains - the genome download directories. This download method is not recommended if you plan to download - a large file or multiple files from a single directory compared to rsync (see above). You can, - however, use the mget command to download multiple files: mget filename1 - filename2, or mget -a (to download all the files in the directory).
+ The UCSC Genome Browser FTP server contains download directories for all genome versions + currently accessible in the Genome Browser. The FTP URLs + ftp://hgdownload.soe.ucsc.edu/goldenPath/ + or + ftp://hgdownload-euro.soe.ucsc.edu/goldenPath/ + will take you to a directory that contains the genome download directories. This download method + is not recommended if you plan to download a large file or multiple files from a single + directory compared to rsync (see above). You can, however, use the mget command to + download multiple files: mget filename1 filename2, or mget -a + (to download all the files in the directory).
Via the Downloads link:
Click the - Downloads link on the - left side bar on the UCSC Genome Browser home page to display a list of all database + Downloads link on + the left side bar on the UCSC Genome Browser home page to display a list of all database directories available for download. If the data you wish to download pre-dates the assembly - versions listed, look for the data on our Downloads page.
+ versions listed, look for the data on our + Downloads page.

Types of data available

There may be several download directories associated with each version of a genome assembly: the full data set (bigZips), the full data set by chromosome (chromosome), the annotation database tables (database), and one or more sets of comparative cross-species alignments.

BigZips contains the entire draft of the genome in chromosome and/or contig form. Depending on the genome, this directory may contain some or all of the following files: