Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM?
As feedback to the list I have solved my problem below and a number of other issues I have had since then with the "Toolfactory" available now from the Main Tool Shed (shameless plug) that was created Ross Lazarus et al. This tool allowed me to create a tool that was exactly what I wanted (a small scriptlet for R, perl, python, or bash) The process was straight forward, and Ross was also very helpful. Thanks also to John Chilton who helped to add an output option that I needed. http://www.ncbi.nlm.nih.gov/pubmed/23024011 https://www.youtube.com/watch?v=Nzzc9zHZJjE https://wiki.galaxyproject.org/DevNewsBriefs/2012_09_20#Galaxy_Tool_Factory Please be sure and heed the warning about NOT installing it on production Galaxy servers though. Regards, Alistair (p.s. I have no affiliation with the creators of the Toolfactory, but I did find it useful, YMMV) -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Alistair Chilcott Sent: Thursday, 28 August 2014 2:36 PM To: Peter Cock Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM? I guess that is my point .. at a command prompt that can be achieved ( and gives the result they need ) but as far as I can see the same is not true via the Galaxy GUI ( unless there is a tool I am missing) They have 96 separate files to process hence the desire to use a workflow. Regards, Alistair -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: Thursday, 28 August 2014 2:27 PM To: Alistair Chilcott Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM? Do you mean a SAM/BAM file sorted by read name? If so, try samtools sort -n ... instead. Peter On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott wrote: > Hello all, > > My users are trying to use a tool called bismark and it requires an > unsorted SAM file for one of its steps > > Previous steps produce BAM files so we would like to include the tool > BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort > by default and there is no way to alter this behaviour. > > Is there another tool that would convert a BAM to a SAM without sorting it or > can the BAM-to-SAM tool be altered to include a checkbox for an unsorted > result? > > > Regards, > > Alistair > > > ___ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM?
Ah - I missed this was on the Galaxy list, sorry. I think that Galaxy automatically coordinate sorts "bam" files, which is generally a good thing bar cases like yours. This problem has undoubtedly come up before - an "unsortedbam" datatype may be needed... Peter On Thu, Aug 28, 2014 at 1:35 PM, Alistair Chilcott wrote: > I guess that is my point .. at a command prompt that can be > achieved ( and gives the result they need ) but as far as I can > see the same is not true via the Galaxy GUI ( unless there is > a tool I am missing) > > They have 96 separate files to process hence the desire to use a workflow. > > Regards, > > Alistair > > > > > -Original Message- > From: Peter Cock [mailto:p.j.a.c...@googlemail.com] > Sent: Thursday, 28 August 2014 2:27 PM > To: Alistair Chilcott > Cc: galaxy-dev@lists.bx.psu.edu > Subject: Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM? > > Do you mean a SAM/BAM file sorted by read name? > If so, try samtools sort -n ... instead. > > Peter > > On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott > wrote: >> Hello all, >> >> My users are trying to use a tool called bismark and it requires an >> unsorted SAM file for one of its steps >> >> Previous steps produce BAM files so we would like to include the tool >> BAM-to-SAM as a step in the workflow unfortunately it seems to be set to >> sort by default and there is no way to alter this behaviour. >> >> Is there another tool that would convert a BAM to a SAM without sorting it >> or can the BAM-to-SAM tool be altered to include a checkbox for an unsorted >> result? >> >> >> Regards, >> >> Alistair >> >> >> ___ >> 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: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM?
I guess that is my point .. at a command prompt that can be achieved ( and gives the result they need ) but as far as I can see the same is not true via the Galaxy GUI ( unless there is a tool I am missing) They have 96 separate files to process hence the desire to use a workflow. Regards, Alistair -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: Thursday, 28 August 2014 2:27 PM To: Alistair Chilcott Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM? Do you mean a SAM/BAM file sorted by read name? If so, try samtools sort -n ... instead. Peter On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott wrote: > Hello all, > > My users are trying to use a tool called bismark and it requires an > unsorted SAM file for one of its steps > > Previous steps produce BAM files so we would like to include the tool > BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort > by default and there is no way to alter this behaviour. > > Is there another tool that would convert a BAM to a SAM without sorting it or > can the BAM-to-SAM tool be altered to include a checkbox for an unsorted > result? > > > Regards, > > Alistair > > > ___ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM?
Do you mean a SAM/BAM file sorted by read name? If so, try samtools sort -n ... instead. Peter On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott wrote: > Hello all, > > My users are trying to use a tool called bismark and it requires an unsorted > SAM file for one of its steps > > Previous steps produce BAM files so we would like to include the tool > BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort > by default and there is no way to alter this behaviour. > > Is there another tool that would convert a BAM to a SAM without sorting it or > can the BAM-to-SAM tool be altered to include a checkbox for an unsorted > result? > > > Regards, > > Alistair > > > ___ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] BAM to SAM tool no way to get an unsorted SAM?
Hello all, My users are trying to use a tool called bismark and it requires an unsorted SAM file for one of its steps Previous steps produce BAM files so we would like to include the tool BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort by default and there is no way to alter this behaviour. Is there another tool that would convert a BAM to a SAM without sorting it or can the BAM-to-SAM tool be altered to include a checkbox for an unsorted result? Regards, Alistair ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
