Differences

This shows you the differences between two versions of the page.

--- shovill-software [2025/05/06 10:00] – created aorth
+++ shovill-software [2026/07/14 06:11] (current) – external edit 127.0.0.1
@@ Line 38: / Line 38: @@
     trimmomatic/0.39 samclip/0.4.0
 $ shovill --version
-shovill 1.1.0</code>
+shovill 1.1.0
+$ shovill --check
+[shovill] Using bwa - /export/apps/bwa/0.7.18/bin/bwa | Version: 0.7.18-r1243-dirty
+[shovill] Using flash - /export/apps/flash/1.2.11/flash | FLASH v1.2.11
+[shovill] Using java - /usr/bin/java | openjdk version "11.0.20.1" 2023-08-24 LTS
+[shovill] Using kmc - /export/apps/kmc/3.1.1/bin/kmc | K-Mer Counter (KMC) ver. 3.1.1 (2019-05-19)
+[shovill] Using lighter - /export/apps/lighter/1.1.2/bin/lighter | Lighter v1.1.2
+[shovill] Using megahit - /export/apps/megahit/1.2.9/bin/megahit | MEGAHIT v1.2.9
+[shovill] Using megahit_toolkit - /export/apps/megahit/1.2.9/bin/megahit_toolkit | v1.2.9
+[shovill] Using pigz - /usr/bin/pigz | pigz 2.4
+[shovill] Using pilon - /export/apps/pilon/1.24/pilon | Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500
+[shovill] Using samclip - /export/apps/samclip/0.4.0/bin/samclip | samclip 0.4.0
+[shovill] Using samtools - /export/apps/samtools/1.11/bin/samtools | Version: 1.11 (using htslib 1.11)
+[shovill] Using seqtk - /export/apps/seqtk/1.4/bin/seqtk | Version: 1.4-r122
+[shovill] Using skesa - /export/apps/skesa/2.5.1/bin/skesa | SKESA 2.5.1
+[shovill] Using spades.py - /export/apps/spades/3.15/bin/spades.py | SPAdes genome assembler v3.15.5
+[shovill] Using trimmomatic - /export/apps/trimmomatic/0.39/trimmomatic | 0.39
+[shovill] Using velvetg - /export/apps/velvet/1.2.10/velvetg | Version 1.2.10
+[shovill] Using velveth - /export/apps/velvet/1.2.10/velveth | Version 1.2.10</code>