Aspera<\/a> downloader is a program to download datasets from various data providers, for example the NCBI<\/a>, that support use of the ascp fast downloader.<\/p>\n Version 3.3.3 is installed on the CSF.<\/p>\n Details of the licence, restrictions, links to licence docs etc<\/p>\n We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings<\/abbr>.<\/p>\n Load one of the following modulefiles:<\/p>\n If you have an ssh cert \/ key file then it should be possible to run ascp in a batch job – no password will be requested if credentials are supplied in a file. If you do not have a credentials file you may run the command on the login node.<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using:<\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview Aspera downloader is a program to download datasets from various data providers, for example the NCBI, that support use of the ascp fast downloader. Version 3.3.3 is installed on the CSF. Restrictions on use Details of the licence, restrictions, links to licence docs etc Set up procedure We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-108","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/108","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=108"}],"version-history":[{"count":12,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/108\/revisions"}],"predecessor-version":[{"id":10058,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/108\/revisions\/10058"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=108"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
\r\nmodule load apps\/singularity\/aspera\/4.2.5\r\nmodule load tools\/bintools\/aspera\/3.3.3\r\n<\/pre>\n
Running the application<\/h2>\n
Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#SBATCH -p serial\r\n#SBATCH -t 1-0 # A limit to 1 day (of a maximum of 7 days).\r\n\r\nmodule purge\r\nmodule load tools\/bintools\/aspera\/3.3.3\r\n\r\n# Optional: Provide path to our own KEYFILE for out data provider.\r\n# If NOT done, the default asperaweb_id_dsa.openssh will be used.\r\n# Using a keyfile will prevent ascp asking for a password - so\r\n# you must<\/strong> use a keyfile when running as a batch job!\r\n\r\nKEYFILE=~\/path\/to\/keyfile.ssh\r\n\r\nascp -i $KEYFILE -QT -L- -l 1000M ega-box-800@fasp.ega.ebi.ac.uk:. .\r\n #\r\n # Change the remote username and server address\r\n # as required by your data provider\r\n<\/pre>\n
#!\/bin\/bash --login\r\n#$ -cwd # Job will run from the current directory\r\n # NO '#$ -V line' - we load modulefiles in the jobscript\r\n\r\nmodule load tools\/bintools\/aspera\/3.3.3\r\n\r\n# Optional: Provide path to our own KEYFILE for out data provider.\r\n# If NOT done, the default asperaweb_id_dsa.openssh will be used.\r\n# Using a keyfile will prevent ascp asking for a password - so\r\n# you must<\/strong> use a keyfile when running as a batch job!\r\n\r\nKEYFILE=~\/path\/to\/keyfile.ssh\r\n\r\nascp -i $KEYFILE -QT -L- -l 1000M ega-box-800@fasp.ega.ebi.ac.uk:. .\r\n #\r\n # Change the remote username and server address\r\n # as required by your data provider\r\n<\/pre>\n
sbatch scriptname<\/em><\/pre>\n
qsub scriptname<\/em><\/pre>\n
Further info<\/h2>\n
\n
Updates<\/h2>\n