update tools

Author: warrenlr

_includes/software-content.html

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 '''
 Generate and update the software-content.html file for birollab.ca
-3-column layout with improved styling, lighter headers, tighter spacing.
+3-column layout with aligned install blocks and improved styling.
 '''
 import glob
 import os
@@ -15,40 +15,39 @@
 P2 = ' <a href="'
 P3 = '"><img class="git" src="assets/githubicon.svg"></a></span>'
 
-# Smaller, compact install block
-DIV_START = '<div style="text-align:center; margin-top:4px;"><div class="downloadinfo" style="font-size:12px; font-family:monospace; white-space:nowrap;">'
-LINUXBREW_DIV = '<br>{% include linuxbrew-icon.html%}'
-CONDA_DIV = '<br>{% include bioconda-icon.html%}'
-DOCKER_DIV = '<br>{% include docker-icon.html%}'
-DIV_END = '</div></div>'
+# Install block styling (key fix here)
+DIV_START = '<div style="text-align:center; margin-top:4px;">'
+LINE_STYLE = 'style="font-size:12px; font-family:monospace; height:18px; line-height:18px; white-space:nowrap;"'
 
-P4 = '<p style="padding-top:4px; margin:0;">'
-END = '</p></td>'
+LINUXBREW_ICON = '{% include linuxbrew-icon.html%}'
+CONDA_ICON = '{% include bioconda-icon.html%}'
+DOCKER_ICON = '{% include docker-icon.html%}'
 
-def downloads(lin, bio, dock):
-    """Format string with installation options, preserving alignment"""
-    return_string = DIV_START
-
-    if lin:
-        return_string += (LINUXBREW_DIV + lin)
-    else:
-        return_string += "<br>&nbsp;"
+DIV_END = '</div>'
 
-    if bio:
-        return_string += (CONDA_DIV + bio)
-    else:
-        return_string += "<br>&nbsp;"
+P4 = '<p style="padding-top:4px; margin:0;">'
+END = '</p></td>'
 
-    if dock:
-        return_string += (DOCKER_DIV + dock)
+def line(icon, text):
+    """Return a fixed-height line"""
+    if text:
+        return f'<div {LINE_STYLE}>{icon} {text}</div>'
     else:
-        return_string += "<br>&nbsp;"
+        return f'<div {LINE_STYLE}>&nbsp;</div>'
 
-    return return_string + DIV_END
+def downloads(lin, bio, dock):
+    """Aligned 3-line install block"""
+    return (
+        DIV_START +
+        line(LINUXBREW_ICON, lin) +
+        line(CONDA_ICON, bio) +
+        line(DOCKER_ICON, dock) +
+        DIV_END
+    )
 
 
 def write_html(softwareblurbs_path):
-    """Write the software-content.html file with improved layout"""
+    """Write the software-content.html file with aligned layout"""
     categories = defaultdict(list)
 
     # Read tools
@@ -66,11 +65,10 @@ def write_html(softwareblurbs_path):
     # Write HTML
     with open(os.path.join(softwareblurbs_path, "../_includes/software-content.html"), "w+") as software:
 
-        # Tight table layout (removes spacing between cells)
         software.write('<table style="width:100%; table-layout:fixed; border-collapse:collapse;">\n')
 
         for category in sorted(categories.keys()):
-            # Lighter header, larger font, black text
+            # Header
             software.write(
                 '<tr>'
                 '<td colspan="3" style="background-color:#DCEEFF; '
@@ -101,7 +99,7 @@ def write_html(softwareblurbs_path):
 
                 i += 1
 
-            # Pad final row
+            # Pad last row
             if i % 3 != 0:
                 remaining = 3 - (i % 3)
                 for _ in range(remaining):

python/software.py

@@ -4,5 +4,5 @@ https://github.com/birollab/AMPlify
 
 conda install -c bioconda amplify
 docker run quay.io/biocontainers/amplify
-Attentive deep learning model for antimicrobial peptide prediction
+Deep learning model for AMP prediction
 Antimicrobial Peptide (AMP) Discovery

python/softwareNEW.py

@@ -4,5 +4,5 @@ https://github.com/birollab/AMPSeek
 
 
 
-Anti-microbial property, protein structure, toxicity detection
+AMP prediction, 3D structure, toxicity detection
 Antimicrobial Peptide (AMP) Discovery

softwareblurbs/amplify.txt

@@ -4,5 +4,5 @@ https://github.com/birollab/ChopStitch
 
 
 
-De novo exon prediction and splice graph construction
+De novo exon prediction and splice graph
 Genome Analysis

softwareblurbs/ampseek.txt

@@ -4,5 +4,5 @@ https://github.com/birollab/dida
 brew install brewsci/bio/dida
 
 
-Sequence alignment pipeline to distribute indexing/alignments
+Distribution of sequence indexing/alignments
 Genome Analysis

softwareblurbs/chopstitch.txt

@@ -4,5 +4,5 @@ https://github.com/birollab/ntSynt
 
 conda install -c bioconda ntsynt
 docker run quay.io/biocontainers/ntsynt
-Multi-genome synteny detection using minimizer graph mapping
+Multi-genome synteny detection w/minimizers
 Comparative Genomics

softwareblurbs/dida.txt

@@ -4,5 +4,5 @@ https://github.com/birollab/tAMPer
 
 
 
-Toxicity prediction with 3D structure-aware deep learning
+Toxicity prediction w/3D structure-aware deep learning
 Antimicrobial Peptide (AMP) Discovery

softwareblurbs/ntsynt.txt

@@ -4,5 +4,5 @@ https://github.com/birollab/triAMPh
 
 
 
-Heterogeneous graph attention networks in AMP predictions
+Heterogeneous graph networks in AMP predictions
 Antimicrobial Peptide (AMP) Discovery