Mercurial > repos > devteam > kraken_report
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 |
| 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 |