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Eiger: Difference between revisions
→Old way of processing Eiger data with XDS i.e. using H5ToXds: MacOS !!!
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</pre> | </pre> | ||
= | = Slower way of processing Eiger data with XDS i.e. using H5ToXds/eiger2cbf to convert to CBF= | ||
Since the release of NEGGIA, a plugin for XDS that parallelizes the reading of images from HDF5 data, conversion to H5ToXds is not required anymore. The sections below are thus largely obsolete. | Since the release of NEGGIA, a plugin for XDS that parallelizes the reading of images from HDF5 data, conversion to H5ToXds is not required anymore. The sections below are thus largely obsolete. | ||
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#!/bin/bash | #!/bin/bash | ||
# Kay Diederichs 10/2015 | # Kay Diederichs 10/2015 | ||
# 3/2016 adapt for eiger2cbf-linux and | # 3/2016 adapt for eiger2cbf-linux and hdf2mini-cbf | ||
# for the latter see https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;58a4ee1.1603 and | # for the latter see https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;58a4ee1.1603 and | ||
# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;a048b4e8.1603 | # https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;a048b4e8.1603 | ||
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# Recommendation: | # Recommendation: | ||
# - for the fast local directory one should use a RAMdisk (one GB size at most) | # - for the fast local directory one should use a RAMdisk (one GB size at most) | ||
# - /dev/shm seems to be set up for that purpose on most distributions | # - /dev/shm seems to be set up for that purpose on most Linux distributions | ||
# - on MacOS you can set this up as given at http://stackoverflow.com/questions/2033362/does-os-x-have-an-equivalent-to-dev-shm | |||
# | # | ||
tempfile="/dev/shm/H5ToXds${PWD//\//_}.$3" | tempfile="/dev/shm/H5ToXds${PWD//\//_}.$3" | ||