Mercurial > repos > petrn > repeatexplorer

changeset 1:2d43ed150abe draft

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Uploaded
author petrn
date Fri, 20 Dec 2019 08:26:05 +0000
parents f6ebec6e235e
children 94877d063270
files repex_full_clustering.xml repex_tarean.xml seqclust
diffstat 3 files changed, 6 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/repex_full_clustering.xml	Thu Dec 19 13:46:43 2019 +0000
+++ b/repex_full_clustering.xml	Fri Dec 20 08:26:05 2019 +0000
@@ -1,4 +1,4 @@
-<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " >
+<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.6" >
     <stdio>
       <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" />
       <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
@@ -10,6 +10,7 @@
    <requirements>
      <requirement type="package" version="3.7">python</requirement>
      <requirement type="package" version="0.9.1" >pyrserve</requirement>
+     <requirement type="package" version=">956" >last</requirement>
      <requirement type="package">mafft</requirement>
      <requirement type="package">imagemagick</requirement>
      <requirement type="package">blast</requirement>
--- a/repex_tarean.xml	Thu Dec 19 13:46:43 2019 +0000
+++ b/repex_tarean.xml	Fri Dec 20 08:26:05 2019 +0000
@@ -1,4 +1,4 @@
-<tool id="tarean" name="Tandem Repeat Analyzer" >
+<tool id="tarean" name="Tandem Repeat Analyzer"  version="2.3.6" >
     <stdio>
       <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
       <regex match="error" source="stderr" level="fatal" description="Unknown error" />
@@ -9,6 +9,7 @@
     <requirements>
       <requirement type="package" version="3.7">python</requirement>
       <requirement type="package" version="0.9.1" >pyrserve</requirement>
+      <requirement type="package" version=">956" >last</requirement>
       <requirement type="package">mafft</requirement>
       <requirement type="package">imagemagick</requirement>
       <requirement type="package">blast</requirement>
--- a/seqclust	Thu Dec 19 13:46:43 2019 +0000
+++ b/seqclust	Fri Dec 20 08:26:05 2019 +0000
@@ -65,8 +65,9 @@
                 DD=os.path.basename(config.DNA_DATABASE),
                 DDmd5=utils.md5checksum(config.DNA_DATABASE + ".nsq"))
 
-    except subprocess.CalledProcessError:
+    except:
         version_string = "version of pipeline not available!"
+
     LOGGER.info(version_string)
     return version_string