From 4fe0af90e651c8bf2e61fad8589d58406f94c9cf Mon Sep 17 00:00:00 2001
From: IsmailM <ismail.moghul@gmail.com>
Date: Thu, 10 Jun 2021 23:06:44 +0100
Subject: [PATCH] Use mac's md5 if md5sum is not available

Fixes #4

- Also fixes a loop (where it kept on downloading and then deleting, and then downloading... ) if md5sum was not available
---
 README.md               | 11 ++---------
 lib/ncbi-blast-dbs.rake | 28 ++++++++++++++++++++--------
 2 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/README.md b/README.md
index 4acf10a..09a96bc 100644
--- a/README.md
+++ b/README.md
@@ -8,20 +8,13 @@ or re-downloaded if corrupt. Aborted downloads are safely resumed.
 
 `ncbi-blast-dbs` is faster than NCBI's `update_blastdb.pl`. But unlike
 `update_blastdb.pl`, which is a pure Perl script, `ncbi-blast-dbs` delegates
-download and checksum verification to `wget` and `md5sum` and is thus not as
-universal.
+download and checksum verification to `wget` and `md5sum` / `md5` and is thus
+not as universal.
 
 ### Installation
 
     gem install ncbi-blast-dbs
 
-#### Note for macOS users
-
-If `md5sum` command is not present, you can install it using
-[`Homebrew`](https://brew.sh):
-
-    brew install md5sha1sum
-
 ### Usage
 
 #### List available BLAST databases
diff --git a/lib/ncbi-blast-dbs.rake b/lib/ncbi-blast-dbs.rake
index ea58e90..e02af70 100644
--- a/lib/ncbi-blast-dbs.rake
+++ b/lib/ncbi-blast-dbs.rake
@@ -12,14 +12,26 @@ def download(url)
   # the server is newer and if so download the new copy.
   sh "wget -N --no-verbose #{url}"
 
-  # Immediately download md5 and verify the tarball. Re-download tarball if
-  # corrupt; extract otherwise.
-  sh "wget --no-verbose #{url}.md5 && md5sum -c #{file}.md5" do |matched, _|
-    if !matched
-      sh "rm #{file} #{file}.md5"; download(url)
-    else
-      sh "tar xf #{file}"
-    end
+  # Download Md5
+  sh "wget --no-verbose #{url}.md5"
+
+  # Verify the tarball using md5sum or md5
+  if system("which md5sum > /dev/null")
+    matched = system("md5sum -c #{file}.md5")
+  elsif system("which md5 > /dev/null")
+    md5_out = %x[md5 -q #{file}].chomp
+    md5_actual = File.read("#{file}.md5").split[0]
+    matched = md5_out == md5_actual
+  else
+    puts "Cannot find md5sum or md5. Please install md5sum or md5 and try again"
+    exit 1
+  end
+
+  # Re-download tarball if corrupt; extract otherwise.
+  if !matched
+    sh "rm #{file} #{file}.md5"; download(url)
+  else
+    sh "tar xf #{file}"
   end
 end