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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
author imgteam
date Tue, 13 Jan 2026 12:22:18 +0000
parents e07bfdcb1d26
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8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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1 # libcarna
8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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3 ## HTML output
8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
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5 The tool produces HTML output that needs to be added to the allow list.
8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
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8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
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7 ## GPU support
8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
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8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
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9 The following extra Docker parameters are required to run this tool with GPU support:
8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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10 ```bash
8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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11 --gpus all -e NVIDIA_VISIBLE_DEVICES=all -e NVIDIA_DRIVER_CAPABILITIES=graphics,compute
8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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12 ```
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e07bfdcb1d26 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 9abf60fee6ba4f5d4f4a18d8f4d33e6263b3c065
imgteam
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13 Otherwise, the tool runs with software rendering, which is much slower.
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8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
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8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
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15 When using `planemo test`, the full command line is:
8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
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16 ```bash
8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
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17 planemo test --docker --docker_run_extra_arguments \
8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
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18 "--gpus all -e NVIDIA_VISIBLE_DEVICES=all -e NVIDIA_DRIVER_CAPABILITIES=graphics,compute"
8cd3d5261f28 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
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19 ```