# HG changeset patch
# User soranzo
# Date 1401303401 14400
# Node ID 8b8f81d14facd8091118ee2162f96be458ac6121
Uploaded
diff -r 000000000000 -r 8b8f81d14fac cat_paths.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cat_paths.xml Wed May 28 14:56:41 2014 -0400
@@ -0,0 +1,61 @@
+
+ Concatenate all components of a pathset into a single file.
+
+ hadoop-galaxy
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+ #if $use_hadoop
+ dist_cat_paths
+ #else
+ cat_paths
+ #end if
+ #if $delete_source
+ --delete-source
+ #end if
+ $input_pathset $output_path
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+Datasets represented as pathsets can be split in a number of files.
+This tool takes all of them and concatenates them into a single output file.
+
+In your workflow, you'll need to explicitly set the appropriate data format on the
+output dataset with an Action to "Change Datatype".
+
+"Delete remote input data" option
+====================================
+With this option, after the data has been concated into the new Galaxy dataset,
+the original files that were referenced by the pathset are deleted. This effectively
+tells the action to "move" the data instead of a "copying" it and helps
+avoid amassing intermediate data in your Hadoop workspace.
+
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+"Use Hadoop-based program" option
+====================================
+
+With this option you will use your entire Hadoop cluster to simultaneously write
+multiple parts of the final file. For this to be possible, the Hadoop nodes
+must be able to access the Galaxy file space directly. In addition, to achieve
+reasonable results the Galaxy workspace should on a parallel shared file system.
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+
diff -r 000000000000 -r 8b8f81d14fac datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml Wed May 28 14:56:41 2014 -0400
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diff -r 000000000000 -r 8b8f81d14fac dist_text_zipper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/dist_text_zipper.xml Wed May 28 14:56:41 2014 -0400
@@ -0,0 +1,29 @@
+
+ Compress lots of text files on Hadoop
+
+ hadoop-galaxy
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+ hadoop_galaxy
+ --input $input_data
+ --output $output
+ --executable dist_text_zipper
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+This is a Pydoop-based distributed text file compression program.
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diff -r 000000000000 -r 8b8f81d14fac make_pathset.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/make_pathset.xml Wed May 28 14:56:41 2014 -0400
@@ -0,0 +1,57 @@
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+ Create a pathset for a set of files
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+ hadoop-galaxy
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+ make_pathset
+ #if str($paths.source) == 'tool_input'
+ --force-local --data-format $paths.datapaths.ext "$output_path" "$paths.datapaths"
+ #elif str($paths.source) == 'text_box'
+ #if str($paths.filesystem_select) == "local_fs"
+ --force-local
+ #end if
+ #if $paths.data_format
+ --data-format "$paths.data_format"
+ #end if
+ "$output_path" "$paths.datapaths"
+ #else
+ #raise ValueError("BUG!! unknown paths.source value")
+ #end if
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+Create a pathset for a set of files to be used as input for Hadoop tools.
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diff -r 000000000000 -r 8b8f81d14fac put_dataset.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/put_dataset.xml Wed May 28 14:56:41 2014 -0400
@@ -0,0 +1,42 @@
+
+ Copy data from Galaxy storage to Hadoop storage.
+
+ hadoop-galaxy
+
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+ put_dataset
+ #if $workspace != ""
+ --hadoop-workspace "$workspace"
+ #end if
+ #if $use_distcp
+ --distcp
+ #end if
+ "$input_pathset" "$output_path"
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+ This tools copies data from Galaxy's storage to storage that is suitable for
+ Hadoop jobs. An example of a use case may be to copy data from the Galaxy server
+ to HDFS. Whether this tool is required depends on your specific local setup.
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diff -r 000000000000 -r 8b8f81d14fac split_pathset.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/split_pathset.xml Wed May 28 14:56:41 2014 -0400
@@ -0,0 +1,59 @@
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+ Split a pathset according to a regular expression criteria
+
+ hadoop-galaxy
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+ split_pathset '$criteria_expr'
+ #if $anchor_end
+ --anchor-end
+ #end if
+ --expand-levels $expand_levels
+ $input_pathset $output_true $output_false
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+ Splits a pathset according to a regular expression.
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+ You can have the tool expand the paths in the pathset by a certain number
+ of levels prior to testing whether it matches the regular expression.
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+ **Note**: you can't use '$' in your regular expression. To anchor the
+ expression to the end of the path use the checkbox.
+
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+ *Note*: the regular expression must match the path from its beginning.
+
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diff -r 000000000000 -r 8b8f81d14fac tool_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_conf.xml Wed May 28 14:56:41 2014 -0400
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diff -r 000000000000 -r 8b8f81d14fac tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed May 28 14:56:41 2014 -0400
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+ git clone https://github.com/crs4/hadoop-galaxy/
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+ $INSTALL_DIR/lib/python
+ export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH && python setup.py install --prefix=$INSTALL_DIR --install-lib=$INSTALL_DIR/lib/python
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+ $INSTALL_DIR/bin
+ $INSTALL_DIR/lib/python
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