Mercurial > repos > trinity_ctat > ctat_genome_resource_libs_data_manager_3

changeset 3:d5f99ab85747 draft

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Uploaded
author trinity_ctat
date Tue, 01 May 2018 13:32:58 -0400
parents e16ace74e516
children c372930aaba1
files data_manager/add_ctat_resource_lib.xml
diffstat 1 files changed, 12 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/add_ctat_resource_lib.xml	Tue May 01 12:52:50 2018 -0400
+++ b/data_manager/add_ctat_resource_lib.xml	Tue May 01 13:32:58 2018 -0400
@@ -21,14 +21,14 @@
             --output_filename "${out_file}" 
             #if str( $download_question.download ) == "true":
                 --source_url "\"${download_question.source_url}\"" 
-                #if str( ${download_question.force_download} ) == "true":
+                #if str( $download_question.force_download ) == "true":
                     --force_download
                 #end if
             #end if
-            #if str( ${rebuild} ) == "true":
+            #if str( $rebuild ) == "true":
                 --build 
             #end if
-            #if str( ${gmap_build} ) == "true":
+            #if str( $gmap_build ) == "true":
                 --gmap_build 
             #end if
         ]]>
@@ -100,9 +100,16 @@
         When download is true, the files at https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/
         are used as selectors for the user to choose among.
         Specify the Full Path of the location where the CTAT Resource Library should be placed.
-        You will need approximately 60GB of space for this library.
+        You will need approximately 62GB of space for this library.
+        The installation of this tool takes some time, due to building a conda environment for the dependencies.
+        The download extracts the files during the download. The "source_data" files download faster, but then must be built.
+        Building the library from the "source_data" files can take many hours, depending on the resources of your machine.
+        The "plug-n-play" can take considerable time to download, depending on your internet connection. Even with high speed,
+        it is about 25GB that is transfered, so plan accordingly.
+        Neither the "source_data" nor the "plug-n-play" versions have had their gmap index built. If you are not going to be
+        using gmap_fusion, then you can uncheck the gmap-build check box and save the space and time building the index consumes.
         If you already have the library, specify the full path of the location where it exists and leave the download box unchecked.
-        The Reference Genome name may be left empty if downloading. The name will be used as the selector text of the entry in the data table.
+        The Reference Genome name may be left empty if downloading. The filename will then be used as the selector text of the entry in the data table.
         For more information on CTAT Genome Resource Libraries, see <a http="https://github.com/FusionFilter/FusionFilter/wiki">FusionFilter</a>
     </help>
     <code file="add_ctat_resource_lib.py" />