# HG changeset patch
# User ximgchess
# Date 1683040048 0
# Node ID 9b6e931e0de0033c68a8541800c430247b1ae865
# Parent  6b20bd5d489a3c6a31edda11115f7050774dc4e2
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty

diff -r 6b20bd5d489a -r 9b6e931e0de0 tomo/.test.txt.swp
Binary file tomo/.test.txt.swp has changed
diff -r 6b20bd5d489a -r 9b6e931e0de0 tomo/.tomo_reduce.bu.swp
Binary file tomo/.tomo_reduce.bu.swp has changed
diff -r 6b20bd5d489a -r 9b6e931e0de0 tomo/test.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo/test.txt	Tue May 02 15:07:28 2023 +0000
@@ -0,0 +1,34 @@
+I had a Galaxy tool crash repeatedly on Friday and tried a bunch of things, but nothing helped. Today I tried it from scratch and kept notes:
+
+Removed everything in:
+ /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess
+and in:
+/nfs/chess/galaxy-dev/var/dependencies/_conda/envs
+
+Rebooted the ansible
+
+Made sure that the repo in the testtoolshed is up to date.
+
+Reinstall the CHAP tool at:
+https://galaxy-dev.classe.cornell.edu/admin/toolshed
+Watching its progress, I can see that it first clones the tool repo and then installs the tool dependencies.
+When done, I have the following new content in the galaxy tree:
+ls -al /nfs/chess/galaxy-dev/var/dependencies/_conda/envs:
+drwxr-xr-x 3 galaxy galaxy 32 May  1 09:17 .
+drwxr-xr-x 5 galaxy galaxy 52 Apr 28 08:40 ..
+drwxr-xr-x 3 galaxy galaxy 26 May  1 09:18 chap_test_20230411
+
+ls -al /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess:
+drwxr-xr-x  6 galaxy galaxy  317 May  1 10:04 .
+drwxr-xr-x 15 galaxy galaxy  226 Aug 29  2021 ..
+drwxr-xr-x 12 galaxy galaxy  184 May  1 10:03 __ChessAnalysisPipeline@0.0.2
+-rw-r--r--  1 galaxy galaxy    0 May  1 09:18 .conda_envs_dir_test
+drwxr-xr-x 27 galaxy galaxy 4096 May  1 10:02 mulled-v1-0cd3a5ccc731743d38833d0396752d8219d106c20bb3bb478c34e74608ecb1c3
+drwxr-xr-x 26 galaxy galaxy 4096 May  1 09:51 mulled-v1-67ac3841866ce74ad34393f2abb6cc61f6651a9d3f3e677b9821c88c9b0a676e
+drwxr-xr-x 12 galaxy galaxy  184 May  1 10:04 mulled-v1-b1085bc9e4a5d280004f5b197e8295b3ef5167ea9ea22a074defb863f1b86458
+
+When running a Galaxy tool and only when I try to pip install certif-pyspec, it bombs with:
+OSError: [Errno 30] Read-only file system: '__config__.cpython-310.pyc'
+
+See stdout and stderr in:
+/nfs/chess/aux/reduced_data/user/galaxy-dev/jobs/002/2440/outputs
diff -r 6b20bd5d489a -r 9b6e931e0de0 tomo/tomo_reduce.xml
--- a/tomo/tomo_reduce.xml	Mon May 01 13:16:34 2023 +0000
+++ b/tomo/tomo_reduce.xml	Tue May 02 15:07:28 2023 +0000
@@ -6,7 +6,21 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
-        $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3'
+        mkdir tomo_reduce_plots;
+        #if str($map.type_selector) == "yaml"
+            $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
+            cp $input_file map.yaml &&
+            cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml &&
+        #else
+            cp $input_file setup.nex &&
+            cp $tool_config reduce.yaml &&
+        #end if
+        CHAP --config
+        #if str($map.type_selector) == "yaml"
+            $__tool_directory__/pipeline_reduce_yaml.yaml
+        #else
+            $__tool_directory__/pipeline_reduce_nexus.yaml
+        #end if
         ]]>
     </command>
     <configfiles>