cutadapt: README annotate

annotate README @ 9:93d58ffe39f1 draft

Updated to version 1.6

author	lparsons
date	Mon, 06 Oct 2014 14:01:06 -0400
parents	2d6671b10919
children

rev	line source
0 8b064ea16722 Initial version with multiple adapter support Lance Parsons <lparsons@princeton.edu> parents: diff changeset	1 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)
8b064ea16722 Initial version with multiple adapter support Lance Parsons <lparsons@princeton.edu> parents: diff changeset	2
8 2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	3
9 93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	4 Installation - Tool Shed
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	5 ------------------------
8 2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	6
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	7 The recommended way to install cutadapt as a tool in Galaxy is to the use the
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	8 Galaxy Tool Shed (http://wiki.galaxyproject.org/Tool%20Shed).
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	9
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	10 This will allow cutadapt to be installed automatically and keep track of older
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	11 versions of cutadapt and the tool wrapper.
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	12
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	13
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	14 Installation - Manual
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	15 ---------------------
0 8b064ea16722 Initial version with multiple adapter support Lance Parsons <lparsons@princeton.edu> parents: diff changeset	16
9 93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	17 1. Install the cutadapt package and make sure it is in path for Galaxy
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	18
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	19 2. Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	20
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	21 3. Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file
0 8b064ea16722 Initial version with multiple adapter support Lance Parsons <lparsons@princeton.edu> parents: diff changeset	22
9 93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	23 Optional steps to setup and run Galaxy functional tests
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	24
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	25 4. Copy test-data/* to $GALAXY_HOME/test-data/
5 1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options Lance Parsons <lparsons@princeton.edu> parents: 0 diff changeset	26
9 93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	27 5. Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that
5 1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options Lance Parsons <lparsons@princeton.edu> parents: 0 diff changeset	28 contains the tools you want to test. (e.g. 'tool_conf.xml')
9 93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	29
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	30 6. $GALAXY_HOME/run_functional_tests.sh -id cutadapt
5 1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options Lance Parsons <lparsons@princeton.edu> parents: 0 diff changeset	31 See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/
1dada50cca8a Support for cutadapt 0.9.5, added quality trimming and additional output options Lance Parsons <lparsons@princeton.edu> parents: 0 diff changeset	32
0 8b064ea16722 Initial version with multiple adapter support Lance Parsons <lparsons@princeton.edu> parents: diff changeset	33
8 2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	34 Configuration of Adapters
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	35 -------------------------
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	36
9 93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	37 A list of predefined adapters may be specified in the cutadapt_adapters.txt
8 2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	38 file which resides in the tool-data directory underneath the Galaxy root. A sample
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	39 file is provided.
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	40
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation) lparsons parents: 5 diff changeset	41
9 93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	42 Limitations of the Galaxy wrapper
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	43 ---------------------------------
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	44
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	45 Reading adapters from a fasta file is not supported
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	46 Colorspace data support is not implemented
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	47 Only one "Strip suffix" is suppored
0 8b064ea16722 Initial version with multiple adapter support Lance Parsons <lparsons@princeton.edu> parents: diff changeset	48
9 93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	49
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	50 Galaxy Wrapper Development
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	51 --------------------------
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	52
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	53 Author: Lance Parsons <lparsons@princeton.edu>
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	54
93d58ffe39f1 Updated to version 1.6 lparsons parents: 8 diff changeset	55 Repository: [https://bitbucket.org/lance_parsons/cutadapt\_galaxy\_wrapper](https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper)

Mercurial > repos > lparsons > cutadapt

annotate README @ 9:93d58ffe39f1 draft