Update to use RNAformer 0.0.1

ivelet · Jul 4, 2024 · b889e8d · b889e8d
1 parent b535ac5
commit b889e8d
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Showing 2 changed files with 25 additions and 18 deletions.
diff --git a/tools/rna_tools/rnaformer/infer_rnaformer.xml b/tools/rna_tools/rnaformer/infer_rnaformer.xml
@@ -1,4 +1,4 @@
-<tool id="infer_rnaformer" name="@EXECUTABLE" version="@VERSION@" profile="22.05">
+<tool id="infer_rnaformer" name="@EXECUTABLE" version="1.0.0" profile="22.05">
     <description>Predict the secondary structure of an RNA with RNAformer</description>
     <macros>
         <token name="@EXECUTABLE@">RNAformer</token>
@@ -7,9 +7,7 @@
     <expand macro="requirements">
         <requirement type="package" version="1.83">biopython</requirement>
     </expand>
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <command detect_errors="exit_code"><![CDATA[python '$script_file' > '$output'
+    <command detect_errors="exit_code"><![CDATA[python '$script_file' > '$output' 
 ]]></command>
 <configfiles>
         <configfile name="script_file"><![CDATA[import RNAformer
@@ -152,6 +150,7 @@ for sequence in sequences:
 
         print(f"Predicted Structure: {dot_bracket_str_pred}")
 
+
 ]]></configfile>
     </configfiles>
     <inputs>

diff --git a/tools/rna_tools/rnaformer/macros.xml b/tools/rna_tools/rnaformer/macros.xml
@@ -1,24 +1,32 @@
 <macros>
+    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@profile@">22.05</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="0.0.1">rnaformer</requirement>
+             <requirement type="package" version="2.1.2">pytorch</requirement>
+            <requirement type="package" version="0.1.2">loralib</requirement>
+            <requirement type="package" version="0.16.1">torchvision</requirement>
+            <requirement type="package" version="4.66.2">tqdm</requirement>
+            <requirement type="package" version="1.26.4">numpy</requirement>
+            <requirement type="package" version="0.7.0">einops</requirement>
+            <requirement type="package" version="2.2.2">pytorch-lightning</requirement>
+            <requirement type="package" version="24.0">packaging</requirement>
+            <requirement type="package" version="0.43.0">wheel</requirement>
+            <requirement type="package" version="0.9.0">tabulate</requirement>
+            <requirement type="package" version="1.13.0">scipy</requirement>
+            <requirement type="package" version="2.2.2">pandas</requirement>
+            <requirement type="package" version="1.4.2">scikit-learn</requirement>
+            <requirement type="package" version="3.8.4">matplotlib</requirement>
+            <requirement type="package" version="0.20.21">polars</requirement>
+            <requirement type="package" version="2.16.2">tensorboard</requirement>
+            <requirement type="package" version="4.39.3">transformers</requirement>
+            <requirement type="package" version="2.18.0">datasets</requirement>
+            <requirement type="package" version="0.14.0">deepspeed</requirement>
+            <requirement type="package" version="0.5.3">rotary-embedding-torch</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@VERSION@">1.0.0</token>
-    <xml name="version_command">
-        <version_command>@EXECUTABLE@ --version</version_command>
-    </xml>
-
-    <xml name="stdio">
-        <stdio>
-            <exit_code range="1:" />
-            <exit_code range=":-1" />
-            <regex match="Error:" />
-            <regex match="Exception:" />
-        </stdio>
-    </xml>
-
     <xml name="citations">
         <citations>
             <citation type="doi">10.1101/2024.02.12.579881</citation>