| Previous changeset 0:18fe33eb7775 (2018-03-14) Next changeset 2:ee917702dbd8 (2018-09-10) |
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Commit message:
v0.0.6 |
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modified:
README.rst kodoja_search.xml tool-data/kaiju_databases.loc.sample tool-data/kraken_databases.loc.sample |
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removed:
test-data/krakenDB_test/accmap_file.tmp |
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| diff -r 18fe33eb7775 -r 4554fcd4ef6d README.rst --- a/README.rst Wed Mar 14 12:46:57 2018 -0400 +++ b/README.rst Wed Sep 05 10:44:57 2018 -0400 |
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| @@ -45,6 +45,27 @@ in the ``tool-data/`` folder. Sample files are included which explain the tab-based format to use. +For example, using https://doi.org/10.5281/zenodo.1406071 which is the +database provided with Kodoja:: + + $ cd /mnt/shared/data/ + $ mkdir kodojaDB_v1.0 + $ cd kodojaDB_v1.0 + $ wget https://zenodo.org/record/1406071/files/kodojaDB_v1.0.tar.gz + $ tar -zxvf kodojaDB_v1.0.tar.gz + +Then update your Galaxy configuration in ``tool-data/kraken_databases.loc`` +to add a line like this:: + + kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kraken), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/krakenDB + +And likewise update ``tool-data/kaiju_databases.loc`` with a line like:: + + kodojaDB_v1.0_kaiju(tab)KodojaDB v1.0 (kaiju), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/kaijuDB + +At the time of writing, reloading the ``*.loc`` files required restarting +the Galaxy server. + History ======= @@ -53,6 +74,9 @@ Version Changes ------- ---------------------------------------------------------------------- v0.0.0 - Initial release covering ``kodoja_search.py`` v0.0.3. +v0.0.4 - Minor update to call ``kodoja_search.py`` v0.0.4. +v0.0.6 - Minor update to call ``kodoja_search.py`` v0.0.6. + - Document installing the Kodoja databases from Zenodo. ======= ====================================================================== |
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| diff -r 18fe33eb7775 -r 4554fcd4ef6d kodoja_search.xml --- a/kodoja_search.xml Wed Mar 14 12:46:57 2018 -0400 +++ b/kodoja_search.xml Wed Sep 05 10:44:57 2018 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="kodoja_search" name="Kodoja database search" version="0.0.0"> +<tool id="kodoja_search" name="Kodoja database search" version="0.0.6"> <description>identify viruses from plant RNA sequencing data</description> <requirements> - <requirement type="package" version="0.0.3">kodoja</requirement> + <requirement type="package" version="0.0.6">kodoja</requirement> </requirements> <version_command>kodoja_search.py --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -53,7 +53,7 @@ </options> </param> <conditional name="single_paired"> - <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired"> + <param name="single_paired_selector" type="select" label="Single or paired reads"> <!-- TODO? <option value="collection">Collection</option> --> @@ -102,8 +102,8 @@ FASTQ/FASTA sequencing run by matching them against both Kraken and Kaiju databases. -The main output is a five column tab-separated table as follows -(tabular format in Galaxy): +The main output is a tab-separated table as follows (tabular format in Galaxy) +with the following columns: 1. Species name 2. Species NCBI taxonomy identifier (TaxID) |
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| diff -r 18fe33eb7775 -r 4554fcd4ef6d tool-data/kaiju_databases.loc.sample --- a/tool-data/kaiju_databases.loc.sample Wed Mar 14 12:46:57 2018 -0400 +++ b/tool-data/kaiju_databases.loc.sample Wed Sep 05 10:44:57 2018 -0400 |
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| @@ -7,7 +7,7 @@ # files named ``kaiju_library.fmi``, ``names.dmp`` and # ``nodes.dmp`` (the later being NCBI taxonomy files). # -# e.g. +# e.g. using the database provided with the kaiju-using tool +# kodoja at https://doi.org/10.5281/zenodo.1406071 # -# plants_dec_2017(tab)Plants (December 2017)(tab)/mnt/shared/kaiju_db/plants_2017_12/ -# +# kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kaiju), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/kaijuDB |
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| diff -r 18fe33eb7775 -r 4554fcd4ef6d tool-data/kraken_databases.loc.sample --- a/tool-data/kraken_databases.loc.sample Wed Mar 14 12:46:57 2018 -0400 +++ b/tool-data/kraken_databases.loc.sample Wed Sep 05 10:44:57 2018 -0400 |
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| @@ -8,7 +8,7 @@ # sub-directory named taxonomy containing files from the # NCBI named ``names.dmp`` and ``nodes.dmp`` # -# e.g. +# e.g. using the database provided with the kraken-using tool +# kodoja at https://doi.org/10.5281/zenodo.1406071 # -# plants_dec_2017(tab)Plants (December 2017)(tab)/mnt/shared/kraken_db/plants_2017_12/ -# +# kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kraken), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/krakenDB |