Need to updated paths

[rhshah]

@nikhil @buehlere
We recently closed Ian's account and did not realize he had paths from his home directory. My apologies for the trouble. I think I covered all, but please let me know if I did not and there are things still pointing out to /home/johsoni dir in all the templates

Legacy

beagle/runner/operator/access/v1_0_0/legacy/input_template.json.jinja2

Line 37 in 6b8e22c

"picard_path": "/home/johnsoni/vendor_tools/picard-2.8.1.jar",

Should be:

    "picard_path": "juno:///juno/work/access/production/resources/tools/picard/versions/v2.8.1/picard-2.8.1.jar",

beagle/runner/operator/access/v1_0_0/legacy/input_template.json.jinja2

Line 34 in 6b8e22c

"arrg_path": "/home/johnsoni/vendor_tools/AddOrReplaceReadGroups-1.96.jar",

Should be:

    "arrg_path": "juno:///juno/work/access/production/resources/tools/picard/versions/v1.96/picard-tools-1.96/AddOrReplaceReadGroups.jar",

beagle/runner/operator/access/v1_0_0/legacy/input_template.json.jinja2

Line 42 in 6b8e22c

"marianas_path": "/home/johnsoni/vendor_tools/Marianas-1.8.0.jar",

Should be

    "marianas_path": "juno:///juno/work/access/production/resources/tools/marianas/current/Marianas-1.8.1.jar",

beagle/runner/operator/access/v1_0_0/legacy/input_template.json.jinja2

Line 36 in 6b8e22c

"waltz_path": "/home/johnsoni/vendor_tools/Waltz-2.0.jar",

Should be

    "waltz_path": "juno:///juno/work/access/production/resources/tools/waltz/current/Waltz-3.2.0.jar",

MSI

beagle/runner/operator/access/v1_0_0/msi/input_template.json.jinja2

Line 2 in 6b8e22c

"file_path": "/home/johnsoni/miniconda2/envs/ACCESS_test/lib/python2.7/site-packages/cwl_tools/msi",

   "file_path": "/home/accessbot/miniconda3/envs/ACCESS_cmplx_geno_test/lib/python2.7/site-packages/cwl_tools/msi",

snps_and_indels

beagle/runner/operator/access/v1_0_0/snps_and_indels/input_template.json.jinja2

Line 147 in 6b8e22c

"mutect": "/home/johnsoni/vendor_tools/muTect-1.1.5.jar",

Should be:

      "mutect": "juno:///juno/work/access/production/resources/tools/muTect/current/muTect-1.1.5.jar",

[buehlere]

Opened a pull request with the fixes!