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Updated for cutadapt 0.9.4, no longer need python wrapper
author Lance Parsons <lparsons@princeton.edu>
date Wed, 25 May 2011 18:54:09 -0400
parents 8b064ea16722
children 1dada50cca8a
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8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
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1 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)
8b064ea16722 Initial version with multiple adapter support
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2
8b064ea16722 Initial version with multiple adapter support
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3 Installation
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4 ------------
8b064ea16722 Initial version with multiple adapter support
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5
8b064ea16722 Initial version with multiple adapter support
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6 1 - Install the cutadapt package and make sure it is in path for Galaxy
8b064ea16722 Initial version with multiple adapter support
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7 2 - Copy cutadapt.xml and cutadapt_galaxy_wrapper.py to $GALAXY_HOME/tools/cutadapt
8b064ea16722 Initial version with multiple adapter support
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8 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file
8b064ea16722 Initial version with multiple adapter support
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8b064ea16722 Initial version with multiple adapter support
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11 Limitations
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12 -----------
8b064ea16722 Initial version with multiple adapter support
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13
8b064ea16722 Initial version with multiple adapter support
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14 Colorspace data is not implemented
8b064ea16722 Initial version with multiple adapter support
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15 Discard trimmed reads is not implemented (broken in cutadapt 0.9.3)
8b064ea16722 Initial version with multiple adapter support
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16 Storing of "rest fo read" after the adapter (-r), too-short reads (--too-short-output), and untrimmed-reads (--untreimmed-output) are not implemented
8b064ea16722 Initial version with multiple adapter support
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17 Quality cutoff (-q) not implemented
8b064ea16722 Initial version with multiple adapter support
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18 Prefix and Suffix to read names not implemented
8b064ea16722 Initial version with multiple adapter support
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19 Length-tag addition to read name not implemented