#SAMTOOLS INSTALL LIBZMA DEVELOPEMTN FILES NOT FOUND HOW TO#
The 18.05 pre-release is currently on Main now and a notification about that and how to communicate end-user problems encountered are in the top banner on the server.
In the end, we create/announce the official release with detailed release notes. We do our best to catch problems with local install tests first, then publically host the pre-release on the Test server and test there, and after that host it at Main ( ) and continue testing/fixing things until stable. 18.05 will also be a big release with many upgrades. ġ8.01 was our largest release to date with many upgrades, so it includes a bit more post-initial-release backported fixes than usual. Examples of what we use for Galaxy Main and backend infrastructure for that server are in the other repositories under with "ansible" in the name. Stop Galaxy, update, then start it up again along with any associated services as needed. Get all new changesets or just those you think you need (if any). Set up Git for repo notifications if that helps. To capture all backported changes, admins should be checking those updates at regular intervals and updating as needed. New functionality is not introduced, just fixes.
The back-ported updates to 18.01 are added back into the base release, and only after careful consideration about the impact. The Github repository shows the history/date of all changes made - including those back-ported. Thanks for reporting the problem! Jen, Galaxy team It is better to use release branches announced here. I would strongly discourage you from upgrading to the 18.05 pre-release - much is still in flux. If anything doesn't check out, updates will post back to the same ticket.Īlso please let us know if you problems continue (with new dataset uploads/jobs runs) after you update/restart. I expect to be closing this ticket out later today or tomorrow once done. I'm rerunning a few of the derivative tests but this will take some time to complete (against 18.05 pre-release loaded at now, it includes this fix too). Problem ticket and details (I was involved, just didn't link your specific issue back to that set of issues first pass, my apologies!). This will involve a server restart, so you might want to have users to stop running jobs while you do this or at least warning them you are restarting (the server will inaccessible during the restart), then check for and restart/rerun any jobs that need admin intervention. Or, compare what you have now and decide which to get individually. Try updating your server with git to capture the all the point-fixes made since you originally got the distribution. These corrections were important enough to back-port. A fix was made to 18.01 after the initial release when this bug was found. No such file or directory: 'name_sorted_alignment.sam'Īlso throws an error and does not complete but there is no error message.ĪH, Ok, I found the issue. fail to open file name_sorted_alignment.sam
HTSeq: Fatal error: Unknown error occured Sort: invalid option - invalid option - '1' data/galaxy/galaxy/database/jobs_directory/000/86/tool_script.sh: line 41: 8799 Exit 1 hisat2 -p $ -l 6 -o '/data/galaxy/galaxy/database/files/000/dataset_131.dat' (ERR): hisat2-align died with signal 13 (PIPE) invalid BAM binary header (this is not a BAM file). Sort: invalid option - invalid option - 'l' Any ideas on this or perhaps a location in the file structure I can look at for more information? Help is greatly appreciated as I have several users waiting for me to fix this issue. It seems all of the mappers are able to do their thing but after the mapping when the tool attempts to sort the output using samtools "sort" that is when the errors are thrown and the jobs cannot be completed. I suspect my issue is something with samtools, however if I look under "Mange Dependencies" all of these tools show the samtools dependency resolved by Conda and actually each mapper uses different versions of samtools. I am having issues with several mapping tools that utilize samtools and I think I have finally identified some commonality between the errors.