annotate README.rst @ 3:9bdcba262627 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_translate/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
author iuc
date Mon, 07 Aug 2017 17:29:45 -0400
parents 77ca66b1f5e9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
1 Introduction
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
2 ============
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
3
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
4 `Kraken <http://ccb.jhu.edu/software/kraken/>`__ is a taxonomic sequence
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
5 classifier that assigns taxonomic labels to short DNA reads. It does
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
6 this by examining the :math:`k`-mers within a read and querying a
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
7 database with those :math:`k`-mers. This database contains a mapping of
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
8 every :math:`k`-mer in
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
9 `Kraken <http://ccb.jhu.edu/software/kraken/>`__'s genomic library to
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
10 the lowest common ancestor (LCA) in a taxonomic tree of all genomes that
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
11 contain that :math:`k`-mer. The set of LCA taxa that correspond to the
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
12 :math:`k`-mers in a read are then analyzed to create a single taxonomic
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
13 label for the read; this label can be any of the nodes in the taxonomic
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
14 tree. `Kraken <http://ccb.jhu.edu/software/kraken/>`__ is designed to be
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
15 rapid, sensitive, and highly precise. Our tests on various real and
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
16 simulated data have shown
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
17 `Kraken <http://ccb.jhu.edu/software/kraken/>`__ to have sensitivity
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
18 slightly lower than Megablast with precision being slightly higher. On a
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
19 set of simulated 100 bp reads,
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
20 `Kraken <http://ccb.jhu.edu/software/kraken/>`__ processed over 1.3
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
21 million reads per minute on a single core in normal operation, and over
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
22 4.1 million reads per minute in quick operation.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
23
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
24 The latest released version of Kraken will be available at the `Kraken
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
25 website <http://ccb.jhu.edu/software/kraken/>`__, and the latest updates
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
26 to the Kraken source code are available at the `Kraken GitHub
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
27 repository <https://github.com/DerrickWood/kraken>`__.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
28
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
29 If you use `Kraken <http://ccb.jhu.edu/software/kraken/>`__ in your
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
30 research, please cite the `Kraken
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
31 paper <http://genomebiology.com/2014/15/3/R46>`__. Thank you!
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
32
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
33 System Requirements
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
34 ===================
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
35
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
36 Note: Users concerned about the disk or memory requirements should read
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
37 the paragraph about MiniKraken, below.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
38
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
39 - **Disk space**: Construction of Kraken's standard database will
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
40 require at least 160 GB of disk space. Customized databases may
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
41 require more or less space. Disk space used is linearly proportional
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
42 to the number of distinct :math:`k`-mers; as of Feb. 2015, Kraken's
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
43 default database contains just under 6 billion (6e9) distinct
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
44 :math:`k`-mers.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
45
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
46 In addition, the disk used to store the database should be
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
47 locally-attached storage. Storing the database on a network
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
48 filesystem (NFS) partition can cause Kraken's operation to be very
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
49 slow, or to be stopped completely. As NFS accesses are much slower
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
50 than local disk accesses, both preloading and database building will
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
51 be slowed by use of NFS.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
52
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
53 - **Memory**: To run efficiently, Kraken requires enough free memory to
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
54 hold the database in RAM. While this can be accomplished using a
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
55 ramdisk, Kraken supplies a utility for loading the database into RAM
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
56 via the OS cache. The default database size is 75 GB (as of Feb.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
57 2015), and so you will need at least that much RAM if you want to
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
58 build or run with the default database.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
59
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
60 - **Dependencies**: Kraken currently makes extensive use of Linux
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
61 utilities such as sed, find, and wget. Many scripts are written using
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
62 the Bash shell, and the main scripts are written using Perl. Core
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
63 programs needed to build the database and run the classifier are
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
64 written in C++, and need to be compiled using g++. Multithreading is
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
65 handled using OpenMP. Downloads of NCBI data are performed by wget
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
66 and in some cases, by rsync. Most Linux systems that have any sort of
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
67 development package installed will have all of the above listed
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
68 programs and libraries available.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
69
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
70 Finally, if you want to build your own database, you will need to
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
71 install the
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
72 `Jellyfish <http://www.cbcb.umd.edu/software/jellyfish/>`__
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
73 :math:`k`-mer counter. Note that Kraken only supports use of
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
74 Jellyfish version 1. Jellyfish version 2 is not yet compatible with
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
75 Kraken.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
76
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
77 - **Network connectivity**: Kraken's standard database build and
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
78 download commands expect unfettered FTP and rsync access to the NCBI
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
79 FTP server. If you're working behind a proxy, you may need to set
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
80 certain environment variables (such as ``ftp_proxy`` or
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
81 ``RSYNC_PROXY``) in order to get these commands to work properly.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
82
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
83 - **MiniKraken**: To allow users with low-memory computing environments
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
84 to use Kraken, we supply a reduced standard database that can be
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
85 downloaded from the Kraken web site. When Kraken is run with a
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
86 reduced database, we call it MiniKraken.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
87
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
88 The database we make available is only 4 GB in size, and should run
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
89 well on computers with as little as 8 GB of RAM. Disk space required
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
90 for this database is also only 4 GB.
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
91
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
92