Pin Bowtie2 to a working version #51
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Bowtie2 2.4.1, which we get otherwise at the moment, is packaged incorrectly in Bioconda, see <bioconda/bioconda-recipes#22836>.
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Oh I see, that was some great debugging, the SAM header error was not exactly giving that away. |
marcelm
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The reason for restricting the version to 2.3.5.1 was that the tool would create incorrect VN tags in the SAM header, see #51. This bug has since been fixed according to bioconda/bioconda-recipes#22836 . The upstream issue at BenLangmead/bowtie2#301 was re-opened, though. Closes #121
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Bowtie2 2.4.1, which we get otherwise at the moment, is packaged incorrectly in Bioconda, see bioconda/bioconda-recipes#22836.
With this, we no longer get this error message from
je markdupes: