Mercurial > repos > richard-burhans > ncbi_fcs_adaptor
annotate notes.txt @ 0:d55ad8533d58 draft default tip
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
author | richard-burhans |
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date | Fri, 01 Mar 2024 18:26:57 +0000 |
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d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
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1 -rw-r--r-- 1 rico rico 0 Feb 22 20:46 fasta_validation_log.txt |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
parents:
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2 -rw-r--r-- 1 rico rico 15015 Feb 22 20:46 adapter_log.txt |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
parents:
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3 -rw-r--r-- 1 rico rico 1996423 Feb 22 20:46 cleaned.fa |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
parents:
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4 -rw-r--r-- 1 rico rico 36 Feb 22 20:46 adapter_report.tabular |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
parents:
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5 |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
parents:
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6 |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
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7 <!-- |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
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8 $DOCKER run --init --name $CONTAINER --user "$(id -u):$(id -g)" -v $FASTA_DIRNAME:/sample-volume/ \ |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
parents:
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9 -v $EXPANDED_OUTPUT:/output-volume/ $DOCKER_IMAGE \ |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
parents:
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10 /app/fcs/bin/av_screen_x -o /output-volume/ $TAX /sample-volume/$FASTA_FILENAME |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
parents:
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11 |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
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12 singularity run $CONTAINER \ |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
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13 --bind $FASTA_DIRNAME:/sample-volume/ \ |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
parents:
diff
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14 --bind $EXPANDED_OUTPUT:/output-volume/ \ |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
parents:
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15 $SINGULARITY_IMAGE \ |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
parents:
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16 /app/fcs/bin/av_screen_x -o /output-volume/ $TAX /sample-volume/$FASTA_FILENAME |
d55ad8533d58
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor commit 74ccb005520db16be005e6471e8624357aca7d94
richard-burhans
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17 --> |