Thx for this fix!
I came up myself with a similar patch but yours is cleaner ;-)
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readlink error when using abyss-dida aligner
I'm running an assembly with abyss and I wanted to give this new distributed aligner option DIDA a try. Unfortunately it did not ran successfully and I was reported the following error:
readlink: extra operand `/CleanOK/C1MLEACXX_3_0_2.cleanTrim.fq.gz'
Try `readlink --help' for more information.
I googled this and apparently it has been reported as a bug in the DIDA software (https://github.com/bcgsc/abyss/issues/87). I was just wondering if any progress has been made to get this resolved or if there are any workarounds for this issue?
thx, L.
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1 answer
Sorry about that.
I've pushed a fix to the public abyss repo. So if you compile/install from HEAD revision at https://github.com/bcgsc/abyss it should be fixed.
Alternatively, you can manually copy the bin/abyss-dida file from https://github.com/bcgsc/abyss to your ABySS installation directory or apply the following patch:
diff --git a/bin/abyss-dida b/bin/abyss-dida
index 593cfec..31cbc7d 100755
--- a/bin/abyss-dida
+++ b/bin/abyss-dida
@@ -71,7 +71,7 @@ fi
# Add file arguments to dida command. Convert all input file paths
# to absolute, since we change to a temp dir below
-query=($(readlink -f "$@"))
+query=($(echo "$@" | xargs -n1 readlink -f))
target=${query[${#query[@]}-1]}
unset query[${#query[@]}-1]
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