singularity-python

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Using the sed command in Singularity Exec does not work. Similar with Redirect ">" symbol.

6

Command line works as expected: `singularity exec --writable-tmpfs instance://reclusive_cat_2780 sed -i 's/REPLACE_THIS_LINE/ \/Work\/III_mzML\/Dorrestein_GnPS_P14_G10_7V_Rep01_Neg_29Dec20_Fiji_Infusion_Min50_MA-csum-Min20_3.mzML/' /Work/MZmine_FeatureFinder-batch.xml` Python Command doesn't work: file_name = "test_file" command_list_1 = """sed -i \'s/REPLACE_THIS_LINE/ \/Work\/III_mzML\/""" +file_name + """/\'...

jjacobson95

vladdoster

Support more options for singularity run and singularity exec (--pwd)

2

Client.run() and Client.exec() only support a subset of the options available. From the API: variable | example | default | description -- | -- | -- | -- bind |...

namheegordonkim

@cclerget is there a secure build for 2.6 (and beeeyooooond!) :) Before the hurricane I want to update the builders in case we are powerless for a little bit!

vsoch

If a user decides to make a folder named exactly "Singularity" in their upper level directory of the repo (e.g., see this issue https://github.com/gearslaboratory/gears-singularity/issues/1) and the repo associated, the builder...

vsoch

vsoch