flexbar v2.7 & required format extension
Hi, does someone use latest version of flexbar 2.7 with Galaxy? It seems newest flexbar changes way how it works with data. Now it requires format extension for data. But Galaxy operates data with .dat extension in database/files/. Also there is flexbar wrapper for version 2.7, so it should be somehow integrated to the Galaxy. Our Galaxy is 16.04. Thanx, Nikolaos
Hi, You can solve the extension issue using soft links in your tool wrapper. E.g.: ln -s $input_fasta $input_fasta.fna Best, Mina Sent from my iPhone
On Jun 18, 2016, at 12:04, Nikolaos Tur <nikolaos.tur@gmail.com> wrote:
Hi,
does someone use latest version of flexbar 2.7 with Galaxy? It seems newest flexbar changes way how it works with data. Now it requires format extension for data. But Galaxy operates data with .dat extension in database/files/. Also there is flexbar wrapper for version 2.7, so it should be somehow integrated to the Galaxy. Our Galaxy is 16.04.
Thanx, Nikolaos ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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thanx Mina, I thought about this. If no one still did this, question is where to add soft link creation. Probably in flexbar.xml. Now flexbar supports fasta and fastaq format, also their gziped/bziped versions. How to determine data format in Galaxy? I'm not an expert neither in Galaxy nor biology, just try to administrate Galaxy instance. Thanx, Nikolaos On Sat, Jun 18, 2016 at 2:54 PM, Mina Bashir <mina.bashir@medunigraz.at> wrote:
Hi, You can solve the extension issue using soft links in your tool wrapper. E.g.: ln -s $input_fasta $input_fasta.fna
Best, Mina
Sent from my iPhone
On Jun 18, 2016, at 12:04, Nikolaos Tur <nikolaos.tur@gmail.com> wrote:
Hi,
does someone use latest version of flexbar 2.7 with Galaxy? It seems newest flexbar changes way how it works with data. Now it requires format extension for data. But Galaxy operates data with .dat extension in database/files/. Also there is flexbar wrapper for version 2.7, so it should be somehow integrated to the Galaxy. Our Galaxy is 16.04.
Thanx, Nikolaos ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Nikolaos, Exactly, you need to change your too.xml file. You could try to solve this with an if condition: #if isinstance($input_fasta.datatype, $__app__.datatypes_registry.get_datatype_by_extension('fastq').__class__): ln -s $input_fasta $input_fasta.fastq #elif isinstance($input_fasta.datatype, $__app__.datatypes_registry.get_datatype_by_extension('fasta').__class__): ln -s $input_fasta $input_fasta.fastq ## use as many elifs as you need #else: ln -s $input_fasta $input_fasta.fastq.gz #end if Might not be the most elegant way, but I think it should work, assuming that you have added all extensions to datatypes. best, Mina Mina Bashir, MSc Division of Endocrinology & Diabetology Medical University of Graz ZMF Center for Medical Research Stiftingtalstraße 24 8010 Graz, Austria mina.bashir@medunigraz.at <mailto:mina.bashir@medunigraz.at> +43 (0) 316 385 72713
Am 19.06.2016 um 00:51 schrieb Nikolaos Tur <nikolaos.tur@gmail.com>:
thanx Mina, I thought about this. If no one still did this, question is where to add soft link creation. Probably in flexbar.xml. Now flexbar supports fasta and fastaq format, also their gziped/bziped versions. How to determine data format in Galaxy? I'm not an expert neither in Galaxy nor biology, just try to administrate Galaxy instance.
Thanx, Nikolaos
On Sat, Jun 18, 2016 at 2:54 PM, Mina Bashir <mina.bashir@medunigraz.at <mailto:mina.bashir@medunigraz.at>> wrote: Hi, You can solve the extension issue using soft links in your tool wrapper. E.g.: ln -s $input_fasta $input_fasta.fna
Best, Mina
Sent from my iPhone
On Jun 18, 2016, at 12:04, Nikolaos Tur <nikolaos.tur@gmail.com <mailto:nikolaos.tur@gmail.com>> wrote:
Hi,
does someone use latest version of flexbar 2.7 with Galaxy? It seems newest flexbar changes way how it works with data. Now it requires format extension for data. But Galaxy operates data with .dat extension in database/files/. Also there is flexbar wrapper for version 2.7, so it should be somehow integrated to the Galaxy. Our Galaxy is 16.04.
Thanx, Nikolaos ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
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Nikolaos Tur