I set library_import_dir to a path and tried uploading a directory of bam files.  After fixing the situation so galaxy could find samtools in that subshell, I was able to upload links to the history.  But moving things to one directory did not appear to be terribly useful, so I tested what happened if I had subdirectories existing in library import directory.<br>
<br>Test 1 I used folders u1 and u2, each with data, and some data in the root library_import_directory.  After clearing the samtools eror I was presented with a drop-down list with choices &#39;None&#39;, &#39;u1&#39; and &#39;u2&#39;.  Selecting &#39;None&#39; did not result in seeking data but a sharp reminder that I had to pick a directory.  Selecting those directories led to uploads, with the Non-Copy correctly sized and even downloadable from the data library, but NOT usable in the history, because upload.py decided the file did not exist (probably the &#39;path&#39; variable in os.path.exists() line 99).<br>
<br>It also became apparent that the upload would look one level down from the root directory and no further (tested by adding u3 with data and a subdirectory of u3 called v3, also with data.<br><br>So the  current state of affairs is that it is a single directory to which one must move files in order to upload links to a galaxy library or folders thereof..  OR, alternatively, make a directory of links called directory A, and then another directory of links to the links in directory A at the library_import_dir and then ask Galaxy to copy the data.  (Not fully tested yet).<br>
<br>But it is apparent from the UI that more utility was intended.  If I have time, I will help with that.<br><br>Michael Moore<br><br>