Tjelvar Olsson tjelvar-olsson
tjelvar-olsson
/ gist:da8baaa05aa1d19194c546acd028d040
Last active
July 6, 2018 01:10
RSE workshop VM instructions
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| sudo apt-get install -y python virtualenv build-essential python-dev | |
| mkdir olsson && cd olsson | |
| virtualenv dtool | |
| source dtool/bin/activate | |
| pip install dtool dtool-s3 dtool-azure | |
| pip install awscli azure-cli | |
| mkdir datasets | |
| dtool copy https://dtool-demo.s3.amazonaws.com/af6727bf-29c7-43dd-b42f-a5d7ede28337 datasets | |
| dtool copy https://dtool-demo.s3.amazonaws.com/c58038a4-3a54-425e-9087-144d0733387f datasets | |
| dtool copy https://dtool-demo.s3.amazonaws.com/ba92a5fa-d3b4-4f10-bcb9-947f62e652db datasets |
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| https://dtool-demo.s3.amazonaws.com/ba92a5fa-d3b4-4f10-bcb9-947f62e652db |
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| Hyopcotyl3.czi: | |
| wget -O Hyopcotyl3.czi https://ndownloader.figshare.com/files/5398223 | |
| bftools: | |
| wget http://downloads.openmicroscopy.org/bio-formats/5.3.4/artifacts/bftools.zip | |
| unzip bftools | |
| what_happened_to_channels_0_and_2.ome.tif: | |
| ./bftools/bfconvert -range 10 10 Hyopcotyl3.czi what_happened_to_channels_1_and_2.ome.tif |