I uploaded the bam file to galaxy main and get the same error.  I also 
confirmed that the hg19.fa reference does exist in my cloudman instance.  Any 
other ideas?

Thanks,
Iry

From: Dannon Baker <dannon.ba...@gmail.com<mailto:dannon.ba...@gmail.com>>
Date: Wednesday, May 1, 2013 12:38 PM
To: Iry Witham <iry.wit...@jax.org<mailto:iry.wit...@jax.org>>
Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
<galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: Re: [galaxy-dev] Installing FreeBayes via Toolshed: Tool dependency 
installation error

This one may be a little out of my wheelhouse, but did you verify that the 
reference it's trying to use is available?  Does this same job work if you try 
it on galaxy main (if that's an option)?

reference=/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa


On Wed, May 1, 2013 at 8:41 AM, Iry Witham 
<iry.wit...@jax.org<mailto:iry.wit...@jax.org>> wrote:
Hi Dannon,

I was able to get cmake installed and then reinstalled Freebayes just fine.  
However, I now am getting the following error: unable to find FASTA index entry 
for '1'. The resulting files is:

Chrom   Pos     ID      Ref     Alt     Qual    Filter  Info    Format  data
##fileformat=VCFv4.1
##fileDate=20130501
##source=freeBayes version 0.9.6
##reference=/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
##phasing=none
##commandline="freebayes --bam localbam_0.bam --fasta-reference 
/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa --vcf 
/mnt/galaxyData/files/000/dataset_101.dat"
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate 
alleles in called genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in 
called genotypes">
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in 
the range (0,1]">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observations">
##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations">
##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for 
the reference allele: Phred-scaled upper-bounds estimate of the probability of 
observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived 
using Hoeffding's inequality">
##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for 
the alternate allele: Phred-scaled upper-bounds estimate of the probability of 
observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived 
using Hoeffding's inequality">
##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous 
sites: a number between 0 and 1 representing the ratio of reads showing the 
reference allele to all reads, considering only reads from individuals called 
as heterozygous">
##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at 
heterozygous sites: Phred-scaled upper-bounds estimate of the probability of 
observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived 
using Hoeffding's inequality">
##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of 
consecutive repeats of the alternate allele in the reference genome">
##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: 
Phred-scaled upper-bounds estimate of the probability of observing the 
deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's 
inequality">
##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for 
reference observations: Phred-scaled upper-bounds estimate of the probability 
of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived 
using Hoeffding's inequality">
##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: 
Phred-scaled upper-bounds estimate of the probability of observing the 
deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's 
inequality">
##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for 
reference observations: Phred-scaled upper-bounds estimate of the probability 
of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived 
using Hoeffding's inequality">
##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. 
Ratio between depth in samples with each called alternate allele and those 
without.">
##INFO=<ID=XRM,Number=1,Type=Float,Description="Reference allele read mismatch 
rate: The rate of SNPs + MNPs + INDELs in reads supporting the reference 
allele.">
##INFO=<ID=XRS,Number=1,Type=Float,Description="Reference allele read SNP rate: 
The rate of per-base mismatches (SNPs + MNPs) in reads supporting the reference 
allele.">
##INFO=<ID=XRI,Number=1,Type=Float,Description="Reference allele read INDEL 
rate: The rate of INDELs (gaps) in reads supporting the reference allele.">
##INFO=<ID=XAM,Number=A,Type=Float,Description="Alternate allele read mismatch 
rate: The rate of SNPs + MNPs + INDELs in reads supporting the alternate 
allele, excluding the called variant.">
##INFO=<ID=XAS,Number=A,Type=Float,Description="Alternate allele read SNP rate: 
The rate of per-base mismatches (SNPs + MNPs) in reads supporting the alternate 
allele, excluding the called variant.">
##INFO=<ID=XAI,Number=A,Type=Float,Description="Alternate allele read INDEL 
rate: The rate of INDELs (gaps) in reads supporting the alternate allele, 
excluding the called variant.">
##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best 
genotype combination to the second-best.">
##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The best genotype combination 
in the posterior is variant (non homozygous).">
##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG site (either CpG, TpG or 
CpA)">
##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either 
snp, mnp, ins, del, or complex.">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR 
representation of each alternate allele, with the exception that '=' is 
replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the 
first matched base (which is provided by default, per the spec) referred to by 
the CIGAR.">
##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique 
non-reference alleles in called genotypes at this position.">
##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique 
non-reference allele observations per sample with the corresponding alternate 
alleles.">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Phred-scaled discrete HWE prior 
probability of the genotyping across all samples.">
##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of 
observed alternate alleles">
##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of 
observed reference alleles">
##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed 
alternate alleles which are supported by properly paired read fragments">
##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed 
reference alleles which are supported by properly paired read fragments">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the 
Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, 
log10-scaled likelihoods of the data given the called genotype for each 
possible genotype generated from the reference and alternate alleles given the 
sample ploidy">
##FORMAT=<ID=GLE,Number=1,Type=String,Description="Genotype Likelihood 
Explicit, same as GL, but with tags to indicate the specific genotype. For 
instance, 0^-75.22|1^-223.42|0/0^-323.03|1/0^-99.29|1/1^-802.53 represents both 
haploid and diploid genotype likilehoods in a biallelic context">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation 
count">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the 
reference observations">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation 
count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the 
alternate observations">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  unknown



Iry

From: Dannon Baker <dannon.ba...@gmail.com<mailto:dannon.ba...@gmail.com>>
Date: Tuesday, April 30, 2013 1:06 PM
To: Iry Witham <iry.wit...@jax.org<mailto:iry.wit...@jax.org>>
Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
<galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: Re: [galaxy-dev] Installing FreeBayes via Toolshed: Tool dependency 
installation error

Looks like you're missing cmake, a dependency for building FreeBayes.  If 
you're able to install that for your system (available in most package 
managers) you should be good to go.

-Dannon


On Tue, Apr 30, 2013 at 1:03 PM, Iry Witham 
<iry.wit...@jax.org<mailto:iry.wit...@jax.org>> wrote:
Hi All,

I am trying to get Freebayes installed on a cloud man instance from the galaxy 
toolshed.  I have successfully installed the Samtools 0.1.18 package, but the 
freebayes package errors.

The Error is:

Tool shed repository: freebayes
Tool shed repository changeset revision: 28e422c589ac
Tool dependency status: Error
Tool dependency installation error: /bin/sh: cmake: not found
make[1]: *** [../bamtools/lib/libbamtools.a] Error 127
make: *** [all] Error 2
Tool dependency installation directory: 
/mnt/galaxyTools/tools/freebayes/0.9.6_9608597d12e127c847ae03aa03440ab63992fedf/devteam/freebayes/28e422c589ac

I get the following message after the error occurs:

This tool dependency is not installed correctly (see the Tool dependency 
installation error below). Choose Uninstall this tool dependency from the 
Repository Actions menu, correct problems if necessary, and try installing the 
dependency again.

I have followed this procedure and still have the same error.  I have looked at 
the Installation.log file and this is what I found:

#############################################
git clone --recursive 
git://github.com/ekg/freebayes.git<http://github.com/ekg/freebayes.git>
STDOUT
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/.git/
Submodule 'bamtools' 
(git://github.com/pezmaster31/bamtools.git<http://github.com/pezmaster31/bamtools.git>)
 registered for path 'bamtools'
Submodule 'intervaltree' 
(git://github.com/ekg/intervaltree.git<http://github.com/ekg/intervaltree.git>) 
registered for path 'intervaltree'
Submodule 'vcflib' 
(git://github.com/ekg/vcflib.git<http://github.com/ekg/vcflib.git>) registered 
for path 'vcflib'
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/bamtools/.git/
Submodule path 'bamtools': checked out 
'3fe66b92028b60629826d827ee9058405fa7e4be'
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/intervaltree/.git/
Submodule path 'intervaltree': checked out 
'd151b487804861dc9f932e9f1fe4f8c499673cec'
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/.git/
Submodule path 'vcflib': checked out '480d96e16a552d36369dc9cb2b39ceedb260944a'
Submodule 'fastahack' 
(git://github.com/ekg/fastahack.git<http://github.com/ekg/fastahack.git>) 
registered for path 'fastahack'
Submodule 'fsom' 
(git://github.com/ekg/fsom.git<http://github.com/ekg/fsom.git>) registered for 
path 'fsom'
Submodule 'intervaltree' 
(git://github.com/ekg/intervaltree.git<http://github.com/ekg/intervaltree.git>) 
registered for path 'intervaltree'
Submodule 'multichoose' 
(git://github.com/ekg/multichoose.git<http://github.com/ekg/multichoose.git>) 
registered for path 'multichoose'
Submodule 'smithwaterman' 
(git://github.com/ekg/smithwaterman.git<http://github.com/ekg/smithwaterman.git>)
 registered for path 'smithwaterman'
Submodule 'tabixpp' 
(git://github.com/ekg/tabixpp.git<http://github.com/ekg/tabixpp.git>) 
registered for path 'tabixpp'
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/fastahack/.git/
Submodule path 'fastahack': checked out 
'6acaf9875f2dbcdf86c9c690a8d188000e90d388'
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/fsom/.git/
Submodule path 'fsom': checked out '1b888f32c4bd571d1a0bea88d39cd7d7f23ea4b8'
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/intervaltree/.git/
Submodule path 'intervaltree': checked out 
'1290744283cef8076bb8a2968d4899b7228435f4'
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/multichoose/.git/
Submodule path 'multichoose': checked out 
'73d35daa18bf35729b9ba758041a9247a72484a5'
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/smithwaterman/.git/
Submodule path 'smithwaterman': checked out 
'd9724f156c07cf16d00d251bebc20c6383eb6bde'
Initialized empty Git repository in 
/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/tabixpp/.git/
Submodule path 'tabixpp': checked out 'fbdde774adfc79ca75a65b4321b89b67cd81b921'
#############################################

#############################################
git clone --recursive 
git://github.com/ekg/freebayes.git<http://github.com/ekg/freebayes.git>
STDERR

#############################################

#############################################
git checkout 9608597d12e127c847ae03aa03440ab63992fedf
STDOUT
M bamtools
M vcflib
#############################################

#############################################
git checkout 9608597d12e127c847ae03aa03440ab63992fedf
STDERR
Note: checking out '9608597d12e127c847ae03aa03440ab63992fedf'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at 9608597... example pipeline script
#############################################

#############################################
git submodule update --recursive
STDOUT
Submodule path 'bamtools': checked out 
'8a5d6508d8fc52b25c9129037e44cc448bafebc7'
Submodule path 'vcflib': checked out '3f0d5e19596252b858a7f6eff1578e4295f549c8'
Submodule path 'fastahack': checked out 
'd1bcd7a2d52ee0e2823884c8ede22ce228d3c060'
Submodule path 'smithwaterman': checked out 
'2882633a3b89f820d692a9b3316f4891dc3a1ff8'
#############################################

#############################################
git submodule update --recursive
STDERR
warning: unable to rmdir fsom: Directory not empty
#############################################

#############################################
make
STDOUT
cd src && make
make[1]: Entering directory `/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/src'
cd ../bamtools && mkdir -p build && cd build && cmake .. && make
make[1]: Leaving directory `/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/src'
#############################################

#############################################
make
STDERR
/bin/sh: cmake: not found
make[1]: *** [../bamtools/lib/libbamtools.a] Error 127
make: *** [all] Error 2
#############################################

Any ideas on how to resolve this?

Thanks,

Iry Witham


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