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    • Closed Issue created by Gervaise Henry @ghenry

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        • Gervaise Henry changed milestone to %v2.1.1

          changed milestone to %v2.1.1

        • Gervaise Henry added To Do label

          added To Do label

        • Gervaise Henry added Doing label and removed To Do label

          added Doing label and removed To Do label

        • Gervaise Henry added enhancement label

          added enhancement label

        • Gervaise Henry
          Gervaise Henry @ghenry ·
          Author Maintainer

          Remove cellranger 3.0.1 and add 2.2.0

          Need to be based on bcl2fastq image

          I have versions already uploaded to dockerhub and my strategy was:
          /bin/sh -c wget -O etc
          /bin/sh -c tar -xzvf cellranger-x.x.x.tar.gz --directory /opt
          ENV PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/cellranger-x.x.x\

          Versions I want supported with docker containers are:

          cellranger version source
          3.1.0 wget -O cellranger-3.1.0.tar.gz "http://cf.10xgenomics.com/releases/cell-exp/cellranger-3.1.0.tar.gz?Expires=1586943601&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9jZWxsLWV4cC9jZWxscmFuZ2VyLTMuMS4wLnRhci5neiIsIkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTU4Njk0MzYwMX19fV19&Signature=ljncbNBaXD1bWB4ysSQ8IIUHyUsihZVIhj47EA4rHkbMyWMoaUJ8y8TiyoQOQgVz1d09rkwrz0NBGlUG2NNij5WdmT2V2wgbLpSGE6tjL5zYuuJQp8rX4dE~o0RFf201g7AVThAcL~FyC8u9~uzJSCjYhPPsuCsXrkYha21RaE8VtNZlkgxQr9~giRT-JEFBCHFdvIxTTwnZIN~kup~9lq43pe6f4UTjqjt-N9bSmsAauGYskoAeJduRNxisc1aYcRcTuCxxFGmEX2I49iaQ0Z37ejNIAGiE7-Qjal5hMyJa55V8x9t07wktmglsXGLwilc1TDvHFqLk9N0Lr6QRNQ__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"
          3.0.2 wget -O cellranger-3.0.2.tar.gz "http://cf.10xgenomics.com/releases/cell-exp/cellranger-3.0.2.tar.gz?Expires=1586943650&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9jZWxsLWV4cC9jZWxscmFuZ2VyLTMuMC4yLnRhci5neiIsIkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTU4Njk0MzY1MH19fV19&Signature=ev~iqIRHK7o3MiX~ikOMorGJYJ~E0cQS-94rNemhz26He26KGHjPtvk~MR-qYHnLVX72oGrQ0qLHY9TVHKZcD05Xhc3LhpZNM5IqttoSQIyc36ipv4FMAaLtUHeqMBbpepm9bxQ7VvZ~bzX1PQNvijGEA6nEWlJDr9fEweoF87hDnc8XgvkEzkrXNnYKOhwK6-QepQ9I7K17pDrxiptAV~JHn1spIoMQKJgBLu7VKHRkaXeV6~JXEVQX~XcLUW9EXu2XaFJIqk60OclgqOCBrIT9w4T87c4SUITFOVvL5kRmP0CJopvUoiiMmJUIYi8H7RxShFOCYD0lIOTI22rQ-g__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"
          2.2.0 wget -O cellranger-2.2.0.tar.gz "http://cf.10xgenomics.com/releases/cell-exp/cellranger-2.2.0.tar.gz?Expires=1586943767&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9jZWxsLWV4cC9jZWxscmFuZ2VyLTIuMi4wLnRhci5neiIsIkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTU4Njk0Mzc2N319fV19&Signature=lyLpHA4WE6WDZkUDvdXXHIH5o~zcIVXTcm2akx6HTiBiJcXhCbbDBSdKIh0YRreyNUmuJaxx6pyzxsr4Vrhr~DIwquQsoMuX5XECzwJSVZrMIkrGFsuxoIBNEWLLaDnm4hmz1tezaqzCtg6cjhjHUVQHBg1fMXamIftrZiICvB79EPpuFqYp3qU3eNV7Q8CJob1B4cib2Yv66jIVUjm4DNQCN5Y5~6dCbRxwF4Q3JQ4vG9nSEt9Lunz96bmMH8J9m0hYWwXYcCexvzNpzPjhe4xACWzL~rOqZThM5UzNnGHXNBLVnFSiG-a1kbMn98r0FlMNMbt1mGbcY8D04dnb9A__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"
          2.1.1 wget -O cellranger-2.1.1.tar.gz "http://cf.10xgenomics.com/releases/cell-exp/cellranger-2.1.1.tar.gz?Expires=1586943803&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9jZWxsLWV4cC9jZWxscmFuZ2VyLTIuMS4xLnRhci5neiIsIkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTU4Njk0MzgwM319fV19&Signature=BmPuTagpdtTK-CCUKH591voQc-VZ06BbC9bktuZqusr1zOL9DKoiInKJ0eKXtLyIw-XE4HnrLyxfbzSqe34fJFCxzaIuxc0lMS6a7ri8lPWTbSTbsGT17m-5jG16QeOOLi-XKBM9FCt3m5bTLfWOfOsRIsgY3trweSUIUn4ZAdXPnMHyq8zfaBkEoo7QQADcagrflV2w1sLcpZ79XVWrT2QOIMaYtmsPMniDCxpDr5N9M1QYnWjmXbwr~S~09wrRK6bmHpc48hKSn2MHggkdfE4e4eg04~KJIa28CTucjaAK8qrH1PrXcKR70fKFBgNxC2mX6B8SODICI6KunPRouA__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"

          @s181706 can you please make updated versions of these containers please (are we still going with 2.0.0... I don't mind going to 1.0.0 for these and deleting the old ones I have up already as they have never been put into production, @venkat.malladi thoughts?).

          @s181706 you can use the strategy I used above, or whatever you think best practices are... I would love the wget, tar and ENV to all be in a single command line to reduce layers

          @s181706 the commands sent to the image will be:
          hostname
          ulimit -a
          bash
          cellranger
          sed of a file piped into tr piped into sed output to a file

          Edited by Gervaise Henry
        • V
          Venkat Malladi @venkat.malladi ·
          Owner

          @ghenry @s181706 I think that lets just move forward with 2.0.0. I would have liked to go to 1.0.0 but at this point I think we just say we had some lessons learned and we move forward. 2.0.0 is the real production level stuff.

        • Gervaise Henry mentioned in merge request !62 (merged)

          mentioned in merge request !62 (merged)

        • Gervaise Henry closed via merge request !62 (merged)

          closed via merge request !62 (merged)

        • Gervaise Henry mentioned in commit e634ce8e

          mentioned in commit e634ce8e

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