# HG changeset patch
# User devteam
# Date 1429722234 14400
# Node ID 60d9479c58d606d164a0a78766279570083c148b
Uploaded
diff -r 000000000000 -r 60d9479c58d6 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Wed Apr 22 13:03:54 2015 -0400
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+Introduction
+============
+
+[Kraken] is a taxonomic sequence classifier that assigns taxonomic
+labels to short DNA reads. It does this by examining the $k$-mers
+within a read and querying a database with those $k$-mers. This database
+contains a mapping of every $k$-mer in [Kraken]'s genomic library to the
+lowest common ancestor (LCA) in a taxonomic tree of all genomes that
+contain that $k$-mer. The set of LCA taxa that correspond to the $k$-mers
+in a read are then analyzed to create a single taxonomic label for the
+read; this label can be any of the nodes in the taxonomic tree.
+[Kraken] is designed to be rapid, sensitive, and highly precise. Our
+tests on various real and simulated data have shown [Kraken] to have
+sensitivity slightly lower than Megablast with precision being slightly
+higher. On a set of simulated 100 bp reads, [Kraken] processed over 1.3
+million reads per minute on a single core in normal operation, and over
+4.1 million reads per minute in quick operation.
+
+The latest released version of Kraken will be available at the
+[Kraken website], and the latest updates to the Kraken source code
+are available at the [Kraken GitHub repository].
+
+If you use [Kraken] in your research, please cite the [Kraken paper].
+Thank you!
+
+[Kraken]: http://ccb.jhu.edu/software/kraken/
+[Kraken website]: http://ccb.jhu.edu/software/kraken/
+[Kraken paper]: http://genomebiology.com/2014/15/3/R46
+[Kraken GitHub repository]: https://github.com/DerrickWood/kraken
+
+
+System Requirements
+===================
+
+Note: Users concerned about the disk or memory requirements should
+read the paragraph about MiniKraken, below.
+
+* **Disk space**: Construction of Kraken's standard database will require at
+ least 160 GB of disk space. Customized databases may require
+ more or less space. Disk space used is linearly proportional
+ to the number of distinct $k$-mers; as of Feb. 2015, Kraken's
+ default database contains just under 6 billion (6e9) distinct $k$-mers.
+
+ In addition, the disk used to store the database should be
+ locally-attached storage. Storing the database on a network
+ filesystem (NFS) partition can cause Kraken's operation to be
+ very slow, or to be stopped completely. As NFS accesses are
+ much slower than local disk accesses, both preloading and database
+ building will be slowed by use of NFS.
+
+* **Memory**: To run efficiently, Kraken requires enough free memory to
+ hold the database in RAM. While this can be accomplished using a
+ ramdisk, Kraken supplies a utility for loading the database into
+ RAM via the OS cache. The default database size is 75 GB (as of
+ Feb. 2015), and so you will need at least that much RAM if you want
+ to build or run with the default database.
+
+* **Dependencies**: Kraken currently makes extensive use of Linux utilities
+ such as sed, find, and wget. Many scripts are written using the
+ Bash shell, and the main scripts are written using Perl. Core
+ programs needed to build the database and run the classifier are
+ written in C++, and need to be compiled using g++. Multithreading
+ is handled using OpenMP. Downloads of NCBI data are performed by
+ wget and in some cases, by rsync. Most Linux systems that have any
+ sort of development package installed will have all of the above
+ listed programs and libraries available.
+
+ Finally, if you want to build your own database, you will need to
+ install the [Jellyfish] $k$-mer counter. Note that Kraken only
+ supports use of Jellyfish version 1. Jellyfish version 2 is not
+ yet compatible with Kraken.
+
+* **Network connectivity**: Kraken's standard database build and download
+ commands expect unfettered FTP and rsync access to the NCBI FTP
+ server. If you're working behind a proxy, you may need to set
+ certain environment variables (such as `ftp_proxy` or `RSYNC_PROXY`)
+ in order to get these commands to work properly.
+
+* **MiniKraken**: To allow users with low-memory computing environments to
+ use Kraken, we supply a reduced standard database that can be
+ downloaded from the Kraken web site. When Kraken is run with a
+ reduced database, we call it MiniKraken.
+
+ The database we make available is only 4 GB in size, and should
+ run well on computers with as little as 8 GB of RAM. Disk space
+ required for this database is also only 4 GB.
+
+[Jellyfish]: http://www.cbcb.umd.edu/software/jellyfish/
\ No newline at end of file
diff -r 000000000000 -r 60d9479c58d6 kraken-filter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kraken-filter.xml Wed Apr 22 13:03:54 2015 -0400
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+
+
+ by confidence score
+
+
+ macros.xml
+
+
+ "$filtered_output"
+ ]]>
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diff -r 000000000000 -r 60d9479c58d6 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Apr 22 13:03:54 2015 -0400
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+
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+ kraken
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+ export LC_ALL=C && kraken --version
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+ 10.1186/gb-2014-15-3-r46
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+
+ --db ${kraken_database.fields.path}/${kraken_database.fields.name}
+
\ No newline at end of file
diff -r 000000000000 -r 60d9479c58d6 tool-data/kraken_databases.loc.sample
diff -r 000000000000 -r 60d9479c58d6 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Apr 22 13:03:54 2015 -0400
@@ -0,0 +1,8 @@
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diff -r 000000000000 -r 60d9479c58d6 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Apr 22 13:03:54 2015 -0400
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