Changes between Version 3 and Version 4 of SOPs/submittingSequencingToGEO

Timestamp:

02/16/24 10:45:52 (11 months ago)

Author:

gbell

Comment:

--

SOPs/submittingSequencingToGEO

@@ -32 +32 @@
 1. Right before or after your publication is made public, change the GEO access from private to public.  [[br]] [[br]]
 
+To upload your files to GEO, you can use a file transfer program with a graphical interface (as recommended by GEO), or you can use a command-line method on a Whitehead server.  Two options are ftp and ncftp.  In the simplest case, all of your files for submission will be in the same directory.  Start by going to that directory on the WI server and then confirm that the files are actually there.
 
+{{{
+cd /path/to/my/files
+ls
+}}}
+
+Make a connection to the NCBI server using the credentials that you got from NCBI and upload your files.
+
+
+{{{
+# Using FTP
+ftp ftp-private.ncbi.nlm.nih.gov
+# You'll be prompted for your username and password
+name: geoftp
+password: MYPASSWD  # each submission is different
+# Now you should be connected to the GEO server.  Change to the directory you were given
+cd uploads/jsmith_e123ABC
+# Turn off iterative mode (so you don't get asked to confirm every file)
+prompt
+# Upload all of the files in the directory from where you connected to GEO 
+mput *
+# Wait what can be a long time ...
+# After everything is uploaded
+quit
+}}}
+
+{{{
+# Using NCFTP
+ncftp -u geoftp -p MYPASSWD ftp-private.ncbi.nlm.nih.gov
+# Now you should be connected to the GEO server.  Change to the directory you were given
+cd uploads/jsmith_e123ABC
+# Upload all of the directories/files in the directory from where you connected to GEO
+# Note that this (a recursive upload) is something that 'ftp' can't do
+mput -r *
+# Wait what can be a long time ...
+# After everything is uploaded
+quit
+}}}
+
+While you command-line uploading is in progress, you can always open a FTP GUI (like FileZilla) to monitor and/or confirm progress.
+
+