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Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).
author pjbriggs
date Tue, 21 Mar 2017 08:42:05 -0400
parents 141bba0e9a77
children 415a165d92bb
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6:141bba0e9a77 7:6eeacf19a38e
16 ====================== 16 ======================
17 17
18 Installation via the Galaxy Tool Shed will take care of installing the tool wrapper 18 Installation via the Galaxy Tool Shed will take care of installing the tool wrapper
19 and the trimmomatic program and data, and setting the appropriate environment 19 and the trimmomatic program and data, and setting the appropriate environment
20 variables. 20 variables.
21
22 Controlling the available memory
23 ================================
24
25 The default amount of memory avilable to trimmomatic is set to 8GB.
26 To change the default amount of memory you can set the environment variable
27 ``_JAVA_OPTIONS`` to ``-Xmx<amount_of_memory_in_GB>G``. The recommended way to
28 set this is in the job_conf.xml file. To change the available memory to 6GB, a
29 line like the below should be added:
30
31 ``<env id="_JAVA_OPTIONS">-Xmx6G</env>``
32
33 This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``.
21 34
22 Manual Installation 35 Manual Installation
23 =================== 36 ===================
24 37
25 There are two files to install: 38 There are two files to install:
56 ======= 69 =======
57 70
58 ========== ====================================================================== 71 ========== ======================================================================
59 Version Changes 72 Version Changes
60 ---------- ---------------------------------------------------------------------- 73 ---------- ----------------------------------------------------------------------
74 0.36.3 - Fix naming of output collections. Instead of all outputs being called
75 "Trimmomatic on collection NN" these will now be called "Trimmomatic
76 on collection NN: paired" or "Trimmomatic on collection NN: unpaired".
61 0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input 77 0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input
62 the output will also be fastqsanger.gz. 78 the output will also be fastqsanger.gz.
63 - Use $_JAVA_OPTIONS to customize memory requirements. 79 - Use $_JAVA_OPTIONS to customize memory requirements.
64 0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version 80 0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version
65 is still supported for now). 81 is still supported for now).