annotate README.rst @ 1:688428f6800f draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit ce0de4de3fa3fc25c375e378ac84f78452dd61c3
author devteam
date Wed, 05 Aug 2015 12:09:35 -0400
parents f2757ab26483
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
1 Introduction
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
2 ============
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
3
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
4 `Kraken <http://ccb.jhu.edu/software/kraken/>`__ is a taxonomic sequence
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
5 classifier that assigns taxonomic labels to short DNA reads. It does
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
6 this by examining the :math:`k`-mers within a read and querying a
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
7 database with those :math:`k`-mers. This database contains a mapping of
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
8 every :math:`k`-mer in
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
9 `Kraken <http://ccb.jhu.edu/software/kraken/>`__'s genomic library to
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
10 the lowest common ancestor (LCA) in a taxonomic tree of all genomes that
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
11 contain that :math:`k`-mer. The set of LCA taxa that correspond to the
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
12 :math:`k`-mers in a read are then analyzed to create a single taxonomic
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
13 label for the read; this label can be any of the nodes in the taxonomic
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
14 tree. `Kraken <http://ccb.jhu.edu/software/kraken/>`__ is designed to be
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
15 rapid, sensitive, and highly precise. Our tests on various real and
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
16 simulated data have shown
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
17 `Kraken <http://ccb.jhu.edu/software/kraken/>`__ to have sensitivity
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
18 slightly lower than Megablast with precision being slightly higher. On a
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
19 set of simulated 100 bp reads,
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
20 `Kraken <http://ccb.jhu.edu/software/kraken/>`__ processed over 1.3
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
21 million reads per minute on a single core in normal operation, and over
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
22 4.1 million reads per minute in quick operation.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
23
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
24 The latest released version of Kraken will be available at the `Kraken
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
25 website <http://ccb.jhu.edu/software/kraken/>`__, and the latest updates
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
26 to the Kraken source code are available at the `Kraken GitHub
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
27 repository <https://github.com/DerrickWood/kraken>`__.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
28
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
29 If you use `Kraken <http://ccb.jhu.edu/software/kraken/>`__ in your
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
30 research, please cite the `Kraken
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
31 paper <http://genomebiology.com/2014/15/3/R46>`__. Thank you!
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
32
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
33 System Requirements
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
34 ===================
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
35
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
36 Note: Users concerned about the disk or memory requirements should read
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
37 the paragraph about MiniKraken, below.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
38
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
39 - **Disk space**: Construction of Kraken's standard database will
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
40 require at least 160 GB of disk space. Customized databases may
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
41 require more or less space. Disk space used is linearly proportional
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
42 to the number of distinct :math:`k`-mers; as of Feb. 2015, Kraken's
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
43 default database contains just under 6 billion (6e9) distinct
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
44 :math:`k`-mers.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
45
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
46 In addition, the disk used to store the database should be
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
47 locally-attached storage. Storing the database on a network
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
48 filesystem (NFS) partition can cause Kraken's operation to be very
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
49 slow, or to be stopped completely. As NFS accesses are much slower
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
50 than local disk accesses, both preloading and database building will
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
51 be slowed by use of NFS.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
52
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
53 - **Memory**: To run efficiently, Kraken requires enough free memory to
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
54 hold the database in RAM. While this can be accomplished using a
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
55 ramdisk, Kraken supplies a utility for loading the database into RAM
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
56 via the OS cache. The default database size is 75 GB (as of Feb.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
57 2015), and so you will need at least that much RAM if you want to
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
58 build or run with the default database.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
59
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
60 - **Dependencies**: Kraken currently makes extensive use of Linux
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
61 utilities such as sed, find, and wget. Many scripts are written using
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
62 the Bash shell, and the main scripts are written using Perl. Core
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
63 programs needed to build the database and run the classifier are
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
64 written in C++, and need to be compiled using g++. Multithreading is
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
65 handled using OpenMP. Downloads of NCBI data are performed by wget
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
66 and in some cases, by rsync. Most Linux systems that have any sort of
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
67 development package installed will have all of the above listed
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
68 programs and libraries available.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
69
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
70 Finally, if you want to build your own database, you will need to
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
71 install the
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
72 `Jellyfish <http://www.cbcb.umd.edu/software/jellyfish/>`__
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
73 :math:`k`-mer counter. Note that Kraken only supports use of
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
74 Jellyfish version 1. Jellyfish version 2 is not yet compatible with
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
75 Kraken.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
76
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
77 - **Network connectivity**: Kraken's standard database build and
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
78 download commands expect unfettered FTP and rsync access to the NCBI
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
79 FTP server. If you're working behind a proxy, you may need to set
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
80 certain environment variables (such as ``ftp_proxy`` or
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
81 ``RSYNC_PROXY``) in order to get these commands to work properly.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
82
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
83 - **MiniKraken**: To allow users with low-memory computing environments
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
84 to use Kraken, we supply a reduced standard database that can be
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
85 downloaded from the Kraken web site. When Kraken is run with a
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
86 reduced database, we call it MiniKraken.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
87
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
88 The database we make available is only 4 GB in size, and should run
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
89 well on computers with as little as 8 GB of RAM. Disk space required
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
90 for this database is also only 4 GB.
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
91
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
92