fixes paths (#66)

* fixes paths * moves yaml path
TheBrownLab · Jan 23, 2023 · d1fc9b3 · d1fc9b3
1 parent c33f9fd
commit d1fc9b3
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Showing 10 changed files with 12 additions and 12 deletions.
diff --git a/phylofisher/envs/bmge.yaml → phylofisher/bmge.yaml b/phylofisher/envs/bmge.yaml → phylofisher/bmge.yaml
diff --git a/phylofisher/envs/divvier.yaml → phylofisher/divvier.yaml b/phylofisher/envs/divvier.yaml → phylofisher/divvier.yaml
diff --git a/phylofisher/envs/gfmix.yaml → phylofisher/gfmix.yaml b/phylofisher/envs/gfmix.yaml → phylofisher/gfmix.yaml
diff --git a/phylofisher/envs/mafft.yaml → phylofisher/mafft.yaml b/phylofisher/envs/mafft.yaml → phylofisher/mafft.yaml
diff --git a/phylofisher/envs/mammal.yaml → phylofisher/mammal.yaml b/phylofisher/envs/mammal.yaml → phylofisher/mammal.yaml
diff --git a/phylofisher/matrix_constructor.smk b/phylofisher/matrix_constructor.smk
@@ -36,7 +36,7 @@ rule prequal:
     log:
         f'{out_dir}/logs/prequal/{{gene}}.log'
     conda:
-        'envs/prequal.yaml'
+        'prequal.yaml'
     shell:
         'prequal {input} >{log} 2>{log}'
 
@@ -49,7 +49,7 @@ rule mafft:
     log:
         f'{out_dir}/logs/mafft/{{gene}}.log'
     conda:
-        'envs/mafft.yaml'
+        'mafft.yaml'
     shell:
         'mafft --thread 1 --globalpair --maxiterate 1000 --unalignlevel 0.6 {input} >{output} 2>{log}'
 
@@ -62,7 +62,7 @@ rule divvier:
     log:
         f'{out_dir}/logs/divvier/{{gene}}.log'
     conda:
-        'envs/divvier.yaml'
+        'divvier.yaml'
     shell:
         f'''
         divvier -minicol 4 -partial {{input}} >{{log}} 2>{{log}}
@@ -79,7 +79,7 @@ rule trimal:
         log:
             f'{out_dir}/logs/trimal/{{gene}}.log'
         conda:
-            'envs/trimal.yaml'
+            'trimal.yaml'
         shell:
             'trimal -in {input} -gt 0.01 -out {output} >{log} 2>{log}'
 

diff --git a/phylofisher/envs/prequal.yaml → phylofisher/prequal.yaml b/phylofisher/envs/prequal.yaml → phylofisher/prequal.yaml
diff --git a/phylofisher/envs/raxml.yaml → phylofisher/raxml.yaml b/phylofisher/envs/raxml.yaml → phylofisher/raxml.yaml
diff --git a/phylofisher/envs/trimal.yaml → phylofisher/trimal.yaml b/phylofisher/envs/trimal.yaml → phylofisher/trimal.yaml
diff --git a/setup.py b/setup.py
@@ -35,14 +35,14 @@
              'phylofisher/utilities/explore_database.py',
              'phylofisher/utilities/gfmix_runner.py',
              'phylofisher/utilities/gfmix_mammal.smk',
-             'phylofisher/envs/gfmix.yaml',
-             'phylofisher/envs/mammal.yaml',
-             'phylofisher/envs/prequal.yaml',
-             'phylofisher/envs/mafft.yaml',
-             'phylofisher/envs/divvier.yaml',
-             'phylofisher/envs/trimal.yaml',
-             'phylofisher/envs/raxml.yaml',
-             'phylofisher/envs/bmge.yaml',
+             'phylofisher/gfmix.yaml',
+             'phylofisher/mammal.yaml',
+             'phylofisher/prequal.yaml',
+             'phylofisher/mafft.yaml',
+             'phylofisher/divvier.yaml',
+             'phylofisher/trimal.yaml',
+             'phylofisher/raxml.yaml',
+             'phylofisher/bmge.yaml',
              },
     url='https://github.com/TheBrownLab/PhyloFisher',
     license='MIT',