# HG changeset patch # User devteam # Date 1437663391 14400 # Node ID 77ca66b1f5e9b6e089900d15eb2faf2eaab60298 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty diff -r 000000000000 -r 77ca66b1f5e9 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Jul 23 10:56:31 2015 -0400 @@ -0,0 +1,92 @@ +Introduction +============ + +`Kraken `__ is a taxonomic sequence +classifier that assigns taxonomic labels to short DNA reads. It does +this by examining the :math:`k`-mers within a read and querying a +database with those :math:`k`-mers. This database contains a mapping of +every :math:`k`-mer in +`Kraken `__'s genomic library to +the lowest common ancestor (LCA) in a taxonomic tree of all genomes that +contain that :math:`k`-mer. The set of LCA taxa that correspond to the +:math:`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! + +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 :math:`k`-mers; as of Feb. 2015, Kraken's + default database contains just under 6 billion (6e9) distinct + :math:`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 `__ + :math:`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. + + diff -r 000000000000 -r 77ca66b1f5e9 kraken-translate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kraken-translate.xml Thu Jul 23 10:56:31 2015 -0400 @@ -0,0 +1,52 @@ + + + convert taxonomy IDs to names + + + macros.xml + + + "${translated}" + ]]> + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 77ca66b1f5e9 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jul 23 10:56:31 2015 -0400 @@ -0,0 +1,30 @@ + + + + + kraken + + + + + + + + + export LC_ALL=C && kraken --version + + + + + + + + + + + 10.1186/gb-2014-15-3-r46 + + + --db ${kraken_database.fields.name} + export KRAKEN_DB_PATH="${kraken_database.fields.path}" + \ No newline at end of file diff -r 000000000000 -r 77ca66b1f5e9 tool-data/kraken_databases.loc.sample diff -r 000000000000 -r 77ca66b1f5e9 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jul 23 10:56:31 2015 -0400 @@ -0,0 +1,8 @@ + + + + + value, name, path + +
+
diff -r 000000000000 -r 77ca66b1f5e9 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jul 23 10:56:31 2015 -0400 @@ -0,0 +1,6 @@ + + + + + +