hal2assemblyHub.py failing to find Bio when run from progressiveCactus with "import source"

[benedictpaten]

Having run "source environment" I get an import error for Bio when running hal2assemblyhub.py, i.e.:

benedict@kolossus progressiveCactus]$ python submodules/hal/bin/hal2assemblyHub.py --help

Usage: hal2assemblyHub.py [options]

[benedict@kolossus progressiveCactus]$ source environment (python)[benedict@kolossus progressiveCactus]$ python submodules/hal/bin/hal2assemblyHub.py --help Traceback (most recent call last): File "submodules/hal/bin/hal2assemblyHub.py", line 28, in from hal.assemblyHub.prepareHubFiles import * File "/hive/users/benedict/progressiveCactus/submodules/hal/assemblyHub/prepareHubFiles.py", line 16, in from Bio import Phylo ImportError: No module named Bio (python)[benedict@kolossus progressiveCactus]$

[joelarmstrong]

Ngan probably knows more about this, but I think we decided not to distribute the Bio (biopython, i think?) library in progressiveCactus. I thought that the library was only used for tree-drawing, but I guess not. We should find a way to load it only if a tree image is needed.

That said, it should be installed already if you're using the recon python.

[benedictpaten]

Oh, yeah, I have it outside of progressive cactus - but this would confused a user coming to progressive cactus fresh.

On Tue, Jul 1, 2014 at 12:40 PM, Joel Armstrong notifications@github.com wrote:

Ngan probably knows more about this, but I think we decided not to distribute the Bio (biopython, i think?) library in progressiveCactus. I thought that the library was only used for tree-drawing, but I guess not. We should find a way to load it only if a tree image is needed.

That said, it should be installed already if you're using the recon python.

— Reply to this email directly or view it on GitHub https://github.com/glennhickey/progressiveCactus/issues/21#issuecomment-47700835 .

[joelarmstrong]

Glenn fixed this a few days ago, thanks Glenn.

[ammeyer]

Hi all - just started using progressiveCactus and this is currently an issue for me - same traceback call:

(python)abrialmeyer~/Desktop/progressiveCactus/work :hal2assemblyHub.py lcb.hal outdir Traceback (most recent call last): File "/Users/abrialmeyer/Desktop/progressiveCactus/submodules/hal/bin/hal2assemblyHub.py", line 28, in from hal.assemblyHub.prepareHubFiles import * File "/Users/abrialmeyer/Desktop/progressiveCactus/submodules/hal/assemblyHub/prepareHubFiles.py", line 16, in from Bio import Phylo ImportError: No module named Bio

can i do anything to fix this?

[ammeyer]

I resolved this issue by bringing to Bio subfolder of biopython in the submodules folder up a level - into the submodules folder. Additionally, for hal2assemblyHub to run the jobTree folder has to be deleted if it was created in the progressiveCactus run

[joelarmstrong]

Sorry that we missed your issue comment before. Glad you ended up resolving it.

We plan to release a totally revamped Cactus "soon-ish" that will take care of a lot of these installation issues--it can definitely be very hard to get it going properly.

[ammeyer]

Hi Joel

Is there a more direct line of communication I could reach you at? My lab group at the American Museum of Natural History is really interested in further use of progressiveCactus. My email is ameyer@amnh.org

Thank you! Abby Meyer

On Tue, Jan 3, 2017 at 7:51 PM, Joel Armstrong notifications@github.com wrote:

Sorry that we missed your issue comment before. Glad you ended up resolving it.

We plan to release a totally revamped Cactus "soon-ish" that will take care of a lot of these installation issues--it can definitely be very hard to get it going properly.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/glennhickey/progressiveCactus/issues/21#issuecomment-270268015, or mute the thread https://github.com/notifications/unsubscribe-auth/AVx_a2DEdvrps8WeT__iurhyyQvIueq6ks5rOu0agaJpZM4CJQSX .

[joelarmstrong]

I'm happy to communicate over email, it's a bit easier for me than github issues. You found my email, but for anyone who comes across this later, my email is jcarmstr@ucsc.edu.

[malcook]

Hi - just saw @ammeyer's workaround after reporting #83 suggesting alternate code fix...