Ok that directory exists but public builds.txt has a .sample at the end.

ubuntu@ip-10-110-143-10:/mnt/galaxyTools/galaxy-central/tool-data/shared/ucsc$ ls

builds.txt builds.txt.sample publicbuilds.txt.sample ucsc_build_sites.txt.new

builds.txt.buildbot manual_builds.txt ucsc_build_sites.txt

ubuntu@ip-10-110-143-10:/mnt/galaxyTools/galaxy-central$ hg tip

Not trusting file /mnt/galaxyTools/galaxy-central/.hg/hgrc from untrusted user galaxy, group galaxy

changeset: 8167:b0c916349070

tag: tip

user: clements

date: Wed Oct 31 23:08:09 2012 -0700

summary: Update docstrings so they no longer generate warnings in Sphix.

ubuntu@ip-10-110-143-10:/mnt/galaxyTools/galaxy-central$ hg st

Not trusting file /mnt/galaxyTools/galaxy-central/.hg/hgrc from untrusted user galaxy, group galaxy

M run.sh

M tool-data/shared/ucsc/ucsc_build_sites.txt

? paster.log

? paster.log.16_06

? paster.log.16_46

? paster.log.17_29

? paster.log.21_01

? paster.log.22_24

? paster.log.22_38

? paster.log.22_42

? paster.pid

? static/images/cloud.gif

? static/images/cloud_text.png

? tool-data/HYPHY

? tool-data/shared/ucsc/ucsc_build_sites.txt.new

? tool_data_table_conf.xml.cloud

? tool_data_table_conf.xml_DEF

ubuntu@ip-10-110-143-10:/mnt/galaxyTools/galaxy-central$ hg diff

Not trusting file /mnt/galaxyTools/galaxy-central/.hg/hgrc from untrusted user galaxy, group galaxy

diff -r b0c916349070 run.sh

--- a/run.sh Wed Oct 31 23:08:09 2012 -0700

+++ b/run.sh Thu Nov 08 19:01:34 2012 +0000

@@ -1,8 +1,9 @@

#!/bin/sh

+export DRMAA_LIBRARY_PATH=/opt/sge/lib/lx24-amd64/libdrmaa.so.1.0

cd `dirname $0`

-python ./scripts/check_python.py

+python -ES ./scripts/check_python.py

[ $? -ne 0 ] && exit 1

SAMPLES="

@@ -17,10 +18,7 @@

tool_sheds_conf.xml.sample

openid_conf.xml.sample

universe_wsgi.ini.sample

- tool-data/shared/ncbi/builds.txt.sample

- tool-data/shared/ensembl/builds.txt.sample

tool-data/shared/ucsc/builds.txt.sample

- tool-data/shared/ucsc/publicbuilds.txt.sample

tool-data/shared/igv/igv_build_sites.txt.sample

tool-data/shared/rviewer/rviewer_build_sites.txt.sample

tool-data/*.sample

@@ -36,20 +34,16 @@

done

-if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then

- python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR"

-fi

# explicitly attempt to fetch eggs before running

FETCH_EGGS=1

for arg in "$@"; do

[ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0; break

done

if [ $FETCH_EGGS -eq 1 ]; then

- python ./scripts/check_eggs.py -q

+ python -ES ./scripts/check_eggs.py -q

if [ $? -ne 0 ]; then

echo "Some eggs are out of date, attempting to fetch..."

- python ./scripts/fetch_eggs.py

+ python -ES ./scripts/fetch_eggs.py

if [ $? -eq 0 ]; then

echo "Fetch successful."

else

@@ -68,8 +62,8 @@

for server in $servers; do

echo "Handling $server with log file $server.log..."

- python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@

+ python -ES ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@

done

else

- python ./scripts/paster.py serve universe_wsgi.ini $@

+ python -ES ./scripts/paster.py serve universe_wsgi.ini $@

diff -r b0c916349070 tool-data/shared/ucsc/ucsc_build_sites.txt

--- a/tool-data/shared/ucsc/ucsc_build_sites.txt Wed Oct 31 23:08:09 2012 -0700

+++ b/tool-data/shared/ucsc/ucsc_build_sites.txt Thu Nov 08 19:01:34 2012 +0000

@@ -1,5 +1,5 @@

#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn

-main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,felCat3,apiMel2,monDom4,apiMel1,ce2

+main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,felCat3,apiMel2,monDom4,apiMel1,ce2,hg19

#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn

archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00

#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn

On 11/8/12 1:55 PM, "Dannon Baker" <dannonbaker@me.com> wrote:

That path should resolve to /mnt/galaxyTools/galaxy-central/tool-data/shared/ucsc/ (or ensembl, ncbi, etc)

Can you tell me the output of 'hg tip' 'hg st' and 'hg diff' from the root /mnt/galaxyTools/galaxy-central/ ?

On Nov 8, 2012, at 1:41 PM, Scooter Willis <HWillis@scripps.edu> wrote:

Errors are being output to stdout

The files don't exist and complicated by the /../../ where I don't know

which subdirectory to follow. Attached screen shot of job failing giving

the ERROR message in the web gui. I also get the same errors when

attempting to run Abys which doesn't run because it isn't installed.

galaxy@ip-10-110-143-10:/mnt/galaxyTools/galaxy-central/lib/galaxy/util$

find -name publicbuilds.txt

galaxy@ip-10-110-143-10:/mnt/galaxyTools/galaxy-central/lib/galaxy/util$ ls

aliaspickler.py debugging.py hash_util.py __init__.py

lrucache.pyc odict.pyc streamball.py topsort.pyc

aliaspickler.pyc docutils_ext hash_util.pyc __init__.pyc

memdump.py sanitize_html.py streamball.pyc

backports docutils_template.txt heartbeat.py json.py

none_like.py sanitize_html.pyc template.py

bunch.py expressions.py inflection.py json.pyc

none_like.pyc shed_util.py template.pyc

bunch.pyc expressions.pyc inflection.pyc lrucache.py

odict.py shed_util.pyc topsort.py

On 11/8/12 1:34 PM, "Dannon Baker" <dannonbaker@me.com> wrote:

Glad to help. The first step would be to check and see if those files

actually exist (and they should).

If those messages are occurring on stdout and not stderr though, they

shouldn't be causing failed jobs and something else might be wrong.

On Nov 8, 2012, at 1:27 PM, Scooter Willis <HWillis@scripps.edu> wrote:

Thanks! That was the explanation I was looking for and the link for how

Do you have any suggestions for fixing the error that are still

after running Bowtie?

Sequence file aligned.

ERROR: Unable to read builds file: [Errno 2] No such file or directory:

'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-data/share

ucsc/publicbuilds.txt'

ERROR: Unable to read builds file: [Errno 2] No such file or directory:

'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-data/share

ERROR: Unable to read builds file: [Errno 2] No such file or directory:

'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-data/share

On 11/8/12 12:44 PM, "Dannon Baker" <dannonbaker@me.com> wrote:

You do not need to restart or add/remove worker nodes, the master's

and data volumes are shared via NFS.

The easiest way to make this work for you in the cloud is probably

to be installing the version of the Abyss binaries you'd like to use

manually in /mnt/galaxyTools/abyss/<version>/ using galaxy's dependency

then, after it has been installed, modify the abyss wrapper to include

<requirement type="package">abyss</requirement> tag, and finally

changes to galaxyTools (which will also restart Galaxy, reloading the

On Nov 8, 2012, at 12:09 PM, Scooter Willis <HWillis@scripps.edu>

If I install abyss to the galaxy tools volume and use cloud admin to

snapshot I assume I then need to remove and then add compute nodes?

the EC2 management console I see two 15GiB EBS volumes from the same

snapshot and I have a master and one compute node running. The other

approach is that the compute nodes have a NFS mount back into the

galaxy_tools volume. Trying to make sure I understand the need to

the compute nodes after an install of third party tools.

From looking at the abyss wrapper it is expecting ABYSS to be found on

path via a .sh file that gets called. Where would I update the path

particular installed tool such that it will be picked up for each

node that gets started? I couldn't find any examples of doing a third

party install with discussion about how that install would persist to

future compute nodes. The missing element for me at the moment is

make path related changes that will be picked up by compute nodes. I

hard code the path in the .sh file used by the wrapper. Just trying to

figure out how to use the software as designed.

On 11/8/12 11:49 AM, "Dannon Baker" <dannonbaker@me.com> wrote:

Neither abyss wrapper in the toolshed installs binaries (you'd see a

tool_dependencies.xml in the repository), that's left up to the end

You might contact the authors of the wrappers via the toolshed to see

they were going to add dependency management and had a newer version,

otherwise you'll have to install binaries on your own. The cloud

do have a version of the Abyss binaries preinstalled, but it's

possible to add a newer version to your particular instance and

the changes to the tool volume (see the cloud admin panel).

On Nov 8, 2012, at 11:20 AM, Scooter Willis <HWillis@scripps.edu>

Ok that fixed Bowtie.

Any thoughts on expected state of installing Abyss from toolshed. It

indicates no requirements so my expectation is that installing from

toolshed should install the appropriate abyss package in a location

tool is expecting to find it.

In looking at the toolshed looks like two wrappers have been

One by msjeon and the other edward-kirton. I did the install for

Is the abyss install located at

/mnt/galaxyTools/tools/abyss/1.2.5/bin

from prior testing and should be deleted. Current release version of

as of May 30 2012 is Abyss 1.3.4

On 11/8/12 11:00 AM, "Dannon Baker" <dannonbaker@me.com> wrote:

Unfortunately the cloud instance upgrade path requires some manual

intervention here due to tool migrations. SSH in to your instance,

/mnt/galaxyTools/galaxy-central/datatypes_conf.xml removing any

references to BlastXML. Save the file, restart galaxy, and you

On Nov 8, 2012, at 10:40 AM, Scooter Willis <HWillis@scripps.edu>

Running a CloudMan created instance on Amazon.

Updated using cloudman from

to version 8167:b0c916349070

Tried to run bowtie and get the following error. Searched the

archives an someone else reported the same problem but thought it

related to a new version of cufflinks. Same problem also exists

running abyss. Given the nature of the error message not even sure

the actual path should be. Also for the abyss install from

toolshed.g2.bx.psu.edu directory doesn't exist or the six

underneath. However Abyss was/is installed at the following

galaxy@ip-10-110-143-10:/mnt/galaxyTools/tools/abyss/1.2.5/bin$

ABYSS abyss-adjtodot abyss-joindist abyss-tofastq

MergePaths PathConsensus SimpleGraph

abyss2ace abyss-fac ABYSS-P AdjList

abyss2afg abyss-fixmate abyss-pe Consensus

ParseAligns PopBubbles

Would be great if someone could give some guidance on how to

the problems. I understand if I need to do something under the

but the expectation is that the one click install/updates should

then require major command line work that isn't documented.

Sequence file aligned.

ERROR: Unable to read builds file: [Errno 2] No such file or

'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat

ed/ucsc/publicbuilds.txt'

ERROR: Unable to read builds file: [Errno 2] No such file or

'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat

ed/ensembl/builds.txt'

ERROR: Unable to read builds file: [Errno 2] No such file or

'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat

WARNING:galaxy.datatypes.registry:Error loading datatype with

extension 'blastxml': 'module' object has no attribute 'BlastXml'

WARNING:galaxy.datatypes.registry:Error appending sniffer for

'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object

attribute 'BlastXml'

Using toolshed installed Abyss and get the same error in Stdout.

ERROR: Unable to read builds file: [Errno 2] No such file or

'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat

ed/ucsc/publicbuilds.txt'

ERROR: Unable to read builds file: [Errno 2] No such file or

'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat

ed/ensembl/builds.txt'

ERROR: Unable to read builds file: [Errno 2] No such file or

'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat

/mnt/galaxyTools/shed_tools/toolshed.g2.bx.psu.edu/repos/msjeon/ab

ol/ce99b6666d1f/abyss_tool/abyss_toolsuite-92636934a189/abyss/abys

per.sh: line 9: ABYSS: command not found

WARNING:galaxy.datatypes.registry:Error loading datatype with

extension 'blastxml': 'module' object has no attribute 'BlastXml'

WARNING:galaxy.datatypes.registry:Error appending sniffer for

'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object

attribute 'BlastXml'

Looking at the util directory based on the expected path of the

galaxy@ip-10-110-143-10:/mnt/galaxyTools/galaxy-central/lib/galaxy

aliaspickler.py docutils_ext heartbeat.py json.pyc

odict.py streamball.py

aliaspickler.pyc docutils_template.txt inflection.py

odict.pyc streamball.pyc

backports expressions.py inflection.pyc

sanitize_html.py template.py

bunch.py expressions.pyc __init__.py

sanitize_html.pyc template.pyc

bunch.pyc hash_util.py __init__.pyc

shed_util.py topsort.py

debugging.py hash_util.pyc json.py

shed_util.pyc topsort.pyc

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