text: user12317: I have multiple .GFF files, each in a single directory per annotated whole genome, that I wish to copy into a single directory so that I can perform a core genome alignment.
  However the following code does not seem to work:
  for pathname in "~/ST_0075/annotations/*/*.gff"; do cp "$pathname" ~/ST_0075/alignment; done
  
  The directory structure is the following:
  Home
  -ST_0075
  ---Annotations
  -----Sample_001
  ----------001.gff
  
  The goal is to copy from multiple Sample_XXX subdirectories within Annotations the XXX.gff files into another directory named alignment
  
  user12317: Tinkered a bit and realized the solution did not neccistate a for loop.
  mkdir ~/ST_0075/alignment; cp ~/ST_0075/annotations/*/*.gff ~/ST_0075/alignment
  
  
original_text: 12317: <p>I have multiple .GFF files, each in a single directory per annotated whole genome, that I wish to copy into a single directory so that I can perform a core genome alignment.</p>
  <p>However the following code does not seem to work:</p>
  <pre><code>for pathname in &quot;~/ST_0075/annotations/*/*.gff&quot;; do cp &quot;$pathname&quot; ~/ST_0075/alignment; done
  </code></pre>
  <p>The directory structure is the following:</p>
  <pre><code>Home
  -ST_0075
  ---Annotations
  -----Sample_001
  ----------001.gff
  </code></pre>
  <p>The goal is to copy from multiple Sample_XXX subdirectories within <code>Annotations</code> the XXX.gff files into another directory named <code>alignment</code></p>
   12317: <p>Tinkered a bit and realized the solution did not neccistate a for loop.</p>
  <pre><code>mkdir ~/ST_0075/alignment; cp ~/ST_0075/annotations/*/*.gff ~/ST_0075/alignment
  </code></pre>
  